I: pbuilder: network access will be disabled during build I: Current time: Mon Mar 10 06:26:24 -12 2025 I: pbuilder-time-stamp: 1741631184 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [pyranges_0.0.111+ds-8.dsc] I: copying [./pyranges_0.0.111+ds.orig.tar.xz] I: copying [./pyranges_0.0.111+ds-8.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./pyranges_0.0.111+ds-8.dsc: unsupported subcommand dpkg-source: info: extracting pyranges in pyranges-0.0.111+ds dpkg-source: info: unpacking pyranges_0.0.111+ds.orig.tar.xz dpkg-source: info: unpacking pyranges_0.0.111+ds-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_dtype.patch dpkg-source: info: applying reorder.patch dpkg-source: info: applying numpy_1.24.patch dpkg-source: info: applying healthcheck-all.patch dpkg-source: info: applying no_install_depends_cython.patch dpkg-source: info: applying pandas2.0.patch dpkg-source: info: applying fix-test_unary.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/13493/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='ee9a5d4ee769426e90886f801a2c5253' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='13493' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.b9NE1NBL/pbuilderrc_1DHT --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.b9NE1NBL/b1 --logfile b1/build.log pyranges_0.0.111+ds-8.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos12-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/13493/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-ncls, python3-pyrle, python3-pytest, python3-pytest-xdist, python3-sorted-nearest, python3-hypothesis, bedtools, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19769 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-ncls; however: Package python3-ncls is not installed. pbuilder-satisfydepends-dummy depends on python3-pyrle; however: Package python3-pyrle is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-xdist; however: Package python3-pytest-xdist is not installed. pbuilder-satisfydepends-dummy depends on python3-sorted-nearest; however: Package python3-sorted-nearest is not installed. pbuilder-satisfydepends-dummy depends on python3-hypothesis; however: Package python3-hypothesis is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-0{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libp11-kit0{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-attr{a} python3-autocommand{a} python3-dateutil{a} python3-execnet{a} python3-hypothesis{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-natsort{a} python3-ncls{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pkg-resources{a} python3-pluggy{a} python3-pyrle{a} python3-pytest{a} python3-pytest-xdist{a} python3-pytz{a} python3-setuptools{a} python3-sorted-nearest{a} python3-sortedcontainers{a} python3-tabulate{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python3-bottleneck python3-bs4 python3-click python3-html5lib python3-jinja2 python3-lxml python3-matplotlib python3-numexpr python3-odf python3-openpyxl python3-pygments python3-scipy python3-tables wget 0 packages upgraded, 109 newly installed, 0 to remove and 0 not upgraded. Need to get 53.2 MB of archives. After unpacking 235 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 libpython3.13-minimal i386 3.13.2-1 [859 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 python3.13-minimal i386 3.13.2-1 [2266 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.13.2-2 [27.1 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 tzdata all 2025a-2 [259 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 libffi8 i386 3.4.7-1 [21.4 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-6 [173 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 libpython3.13-stdlib i386 3.13.2-1 [1985 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 python3.13 i386 3.13.2-1 [745 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.13.2-2 [10.1 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 python3 i386 3.13.2-2 [28.1 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 python3-numpy-dev i386 1:2.2.3+ds-5 [146 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.1-2 [150 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.2.0-17 [735 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.1-2 [2198 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 python3-numpy i386 1:2.2.3+ds-5 [5060 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.23.1-1 [245 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-7 [1199 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.4-5 [96.5 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-7 [301 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 automake all 1:1.17-3 [862 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 autopoint all 0.23.1-1 [770 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 bedtools i386 2.31.1+dfsg-2 [745 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 libtool all 2.5.4-4 [539 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 42 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 libunistring5 i386 1.3-1 [458 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-6 [9582 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b2 [734 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 gettext i386 0.23.1-1 [1714 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 debhelper all 13.24.1 [920 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20250308 [115 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b7 [299 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.2-1 [24.3 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 libidn2-0 i386 2.3.8-1 [110 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 libp11-kit0 i386 0.25.5-3 [423 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 libtasn1-6 i386 4.20.0-2 [51.6 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 libgnutls30t64 i386 3.8.9-2 [1462 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-4 [35.0 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-4 [83.7 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 61 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-4 [354 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-4 [149 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-9 [20.8 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-9 [61.2 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 libldap2 i386 2.6.9+dfsg-1 [205 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 libnghttp3-9 i386 1.8.0-1 [78.7 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 libngtcp2-16 i386 1.11.0-1 [163 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 libngtcp2-crypto-gnutls8 i386 1.11.0-1 [29.9 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 libcurl3t64-gnutls i386 8.12.1-3 [411 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.23-1+b1 [48.4 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 libhtscodecs2 i386 1.6.1-2 [70.9 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 libhts3t64 i386 1.21+ds-1 [506 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 libncurses6 i386 6.5+20250216-2 [112 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 python3-all i386 3.13.2-2 [1044 B] Get: 79 http://deb.debian.org/debian unstable/main i386 python3-attr all 25.1.0-1 [68.7 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 python3-execnet all 2.1.1-1 [40.2 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 python3-hypothesis all 6.127.4-1 [330 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 python3-inflect all 7.3.1-2 [32.4 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 python3-iniconfig all 1.1.1-2 [6396 B] Get: 90 http://deb.debian.org/debian unstable/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 75.8.0-1 [222 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 python3-zipp all 3.21.0-1 [10.6 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 75.8.0-1 [724 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 96 http://deb.debian.org/debian unstable/main i386 python3-natsort all 8.0.2-2 [39.0 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 python3-ncls i386 0.0.63-hotfix+ds-1+b7 [384 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 python3-packaging all 24.2-1 [55.3 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 python3-pytz all 2025.1-3 [150 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 python3-tz all 2025.1-3 [4004 B] Get: 101 http://deb.debian.org/debian unstable/main i386 python3-pandas-lib i386 2.2.3+dfsg-8+b1 [4307 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 python3-pandas all 2.2.3+dfsg-8 [3097 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 python3-pyrle i386 0.0.33-4.1+b3 [290 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 python3-pytest all 8.3.5-1 [250 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 python3-pytest-xdist all 3.6.1-1 [44.4 kB] Get: 108 http://deb.debian.org/debian unstable/main i386 python3-sorted-nearest i386 0.0.39+dfsg-3+b1 [352 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 samtools i386 1.21-1 [700 kB] Fetched 53.2 MB in 1s (60.0 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19769 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_i386.deb ... Unpacking libpython3.13-minimal:i386 (3.13.2-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... 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Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:i386. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_i386.deb ... Unpacking libpython3.13-stdlib:i386 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_i386.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:i386. 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Setting up media-types (13.0.0) ... Setting up libpipeline1:i386 (1.5.8-1) ... Setting up libkeyutils1:i386 (1.6.3-4) ... Setting up libicu72:i386 (72.1-6) ... Setting up bsdextrautils (2.40.4-5) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:i386 (1.1.0-2+b7) ... Setting up libmagic1t64:i386 (1:5.45-3+b1) ... Setting up libnghttp2-14:i386 (1.64.0-1) ... Setting up libdeflate0:i386 (1.23-1+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-7) ... Setting up libcom-err2:i386 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up libkrb5support0:i386 (1.21.3-4) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-9) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Mar 10 18:27:08 UTC 2025. Universal Time is now: Mon Mar 10 18:27:08 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.1-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libncurses6:i386 (6.5+20250216-2) ... Setting up libunistring5:i386 (1.3-1) ... Setting up python3-numpy-dev:i386 (1:2.2.3+ds-5) ... Setting up autopoint (0.23.1-1) ... Setting up libk5crypto3:i386 (1.21.3-4) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-9) ... Setting up libgfortran5:i386 (14.2.0-17) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:i386 (1.8.0-1) ... Setting up libffi8:i386 (3.4.7-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up libtasn1-6:i386 (4.20.0-2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:i386 (1.11.0-1) ... Setting up libkrb5-3:i386 (1.21.3-4) ... Setting up libssh2-1t64:i386 (1.11.1-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Setting up bedtools (2.31.1+dfsg-2) ... Setting up libldap2:i386 (2.6.9+dfsg-1) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:i386 (3.12.1-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-4) ... Setting up libidn2-0:i386 (2.3.8-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libp11-kit0:i386 (0.25.5-3) ... Setting up libgssapi-krb5-2:i386 (1.21.3-4) ... Setting up libreadline8t64:i386 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up libpython3.13-stdlib:i386 (3.13.2-1) ... Setting up libpython3-stdlib:i386 (3.13.2-2) ... Setting up libgnutls30t64:i386 (3.8.9-2) ... Setting up python3.13 (3.13.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:i386 (0.21.2-1.1+b1) ... Setting up python3 (3.13.2-2) ... Setting up python3-sortedcontainers (2.4.0-2) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-natsort (8.0.2-2) ... Setting up python3-packaging (24.2-1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-numpy (1:2.2.3+ds-5) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-ncls (0.0.63-hotfix+ds-1+b7) ... Setting up python3-execnet (2.1.1-1) ... Setting up libngtcp2-crypto-gnutls8:i386 (1.11.0-1) ... Setting up dh-python (6.20250308) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (25.1.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3-pytest (8.3.5-1) ... Setting up python3-pandas-lib:i386 (2.2.3+dfsg-8+b1) ... Setting up python3-hypothesis (6.127.4-1) ... Setting up python3-typeguard (4.4.2-1) ... Setting up libcurl3t64-gnutls:i386 (8.12.1-3) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-all (3.13.2-2) ... Setting up debhelper (13.24.1) ... Setting up python3-pytz (2025.1-3) ... Setting up python3-tz (2025.1-3) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pandas (2.2.3+dfsg-8) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up libhts3t64:i386 (1.21+ds-1) ... Setting up python3-pkg-resources (75.8.0-1) ... Setting up python3-pyrle (0.0.33-4.1+b3) ... Setting up python3-setuptools (75.8.0-1) ... Setting up python3-pytest-xdist (3.6.1-1) ... Setting up python3-sorted-nearest (0.0.39+dfsg-3+b1) ... Setting up samtools (1.21-1) ... Processing triggers for libc-bin (2.41-4) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/pyranges-0.0.111+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pyranges_0.0.111+ds-8_source.changes dpkg-buildpackage: info: source package pyranges dpkg-buildpackage: info: source version 0.0.111+ds-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 dpkg-source: info: using options from pyranges-0.0.111+ds/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/reproducible-path/pyranges-0.0.111+ds' echo 'Generating corresponding files ...' Generating corresponding files ... cat debian/missing-sources/test_sorted.sam| samtools view -Sb - > tests/test_data/test_sorted.bam cat debian/missing-sources/control.sam| samtools view -Sb - > pyranges/example_data/control.bam samtools index tests/test_data/test_sorted.bam tests/test_data/test_sorted.bam.bai samtools index pyranges/example_data/control.bam pyranges/example_data/control.bam.bai make[1]: Leaving directory '/build/reproducible-path/pyranges-0.0.111+ds' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: mkdir -pv /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/*.bed /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/test_data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges '/build/reproducible-path/pyranges-0.0.111+ds/tests/chip_10.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/chip_10.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/f1.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/f1.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/f2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/f2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_data' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_data/test_sorted.bam' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam.bai' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_data/test_sorted.bam.bai' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/ensembl.gtf' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_data/ensembl.gtf' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/gencode.gff3' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_data/gencode.gff3' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/ucsc_df_to_parse.txt' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_data/ucsc_df_to_parse.txt' '/build/reproducible-path/pyranges-0.0.111+ds/tests/data' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/data' '/build/reproducible-path/pyranges-0.0.111+ds/tests/data/test_data.py' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/data/test_data.py' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/control.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/example_data/control.bam' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/lamina.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/example_data/lamina.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/f1.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/example_data/f1.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/bw.bw' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/example_data/bw.bw' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/f2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/example_data/f2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/control.bam.bai' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/example_data/control.bam.bai' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/exons.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/example_data/exons.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ensembl.gtf' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/example_data/ensembl.gtf' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ucsc_human.bed.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/example_data/ucsc_human.bed.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chipseq_background.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/example_data/chipseq_background.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/cpg.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/example_data/cpg.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/gencode_human.gtf.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/example_data/gencode_human.gtf.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chipseq.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/example_data/chipseq.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/aorta.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/example_data/aorta.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ensembl_human.gtf.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/example_data/ensembl_human.gtf.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chromsizes.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/example_data/chromsizes.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/aorta2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/example_data/aorta2.bed' I: pybuild base:311: cd /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build; python3.13 -m pytest -v -n 11 ============================= test session starts ============================== platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 -- /usr/bin/python3.13 cachedir: .pytest_cache hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase(PosixPath('/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/.hypothesis/examples')) rootdir: /build/reproducible-path/pyranges-0.0.111+ds plugins: xdist-3.6.1, hypothesis-6.127.4, typeguard-4.4.2 created: 11/11 workers 11 workers [531 items] scheduling tests via LoadScheduling tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] tests/test_binary.py::test_jaccard[same] tests/test_binary.py::test_k_nearest[upstream-False-same-last] tests/test_binary.py::test_nearest[upstream-True-same] tests/test_binary.py::test_coverage[same] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] tests/data/test_data.py::test_all_data tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] tests/test_change_chromosome_custom.py::test_change_chromosomes [gw4] [ 0%] PASSED tests/test_change_chromosome_custom.py::test_change_chromosomes tests/test_concat.py::test_concat_stranded_unstranded [gw4] [ 0%] PASSED tests/test_concat.py::test_concat_stranded_unstranded tests/test_concat.py::test_concat_unstranded_unstranded [gw4] [ 0%] PASSED tests/test_concat.py::test_concat_unstranded_unstranded tests/test_concat.py::test_concat_unstranded_stranded [gw4] [ 0%] PASSED tests/test_concat.py::test_concat_unstranded_stranded tests/test_count_overlaps.py::test_strand_vs_strand_same [gw4] [ 0%] PASSED tests/test_count_overlaps.py::test_strand_vs_strand_same tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] [gw0] [ 1%] PASSED tests/data/test_data.py::test_all_data tests/test_binary.py::test_set_intersect[False] [gw6] [ 1%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-same-last] tests/test_binary.py::test_k_nearest[upstream-False-False-last] [gw8] [ 1%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain20-method_chain20] [gw10] [ 1%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] [gw4] [ 1%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] [gw5] [ 2%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] [gw7] [ 2%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain32-method_chain32] [gw8] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain20-method_chain20] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] [gw7] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain32-method_chain32] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] [gw9] [ 2%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain44-method_chain44] [gw9] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain44-method_chain44] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain45-method_chain45] [gw9] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain45-method_chain45] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain46-method_chain46] [gw9] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain46-method_chain46] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] [gw10] [ 3%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] [gw6] [ 3%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-False-last] tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] [gw3] [ 3%] FAILED tests/test_binary.py::test_jaccard[same] tests/test_binary.py::test_join[False] [gw5] [ 4%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] [gw7] [ 4%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain34-method_chain34] [gw4] [ 4%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] [gw7] [ 4%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain34-method_chain34] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] [gw0] [ 4%] FAILED tests/test_binary.py::test_set_intersect[False] [gw2] [ 5%] FAILED tests/test_binary.py::test_nearest[upstream-True-same] tests/test_binary.py::test_set_intersect[same] tests/test_binary.py::test_nearest[upstream-True-opposite] [gw9] [ 5%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain48-method_chain48] [gw1] [ 5%] FAILED tests/test_binary.py::test_coverage[same] tests/test_binary.py::test_coverage[opposite] [gw9] [ 5%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain48-method_chain48] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] [gw10] [ 5%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] [gw4] [ 6%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] [gw6] [ 6%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] tests/test_binary.py::test_k_nearest[upstream-True-same-last] [gw5] [ 6%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] [gw7] [ 6%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] [gw6] [ 6%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-same-last] tests/test_binary.py::test_k_nearest[upstream-True-False-last] [gw8] [ 6%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] [gw4] [ 7%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] [gw9] [ 7%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] [gw5] [ 7%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] [gw3] [ 7%] PASSED tests/test_binary.py::test_join[False] [gw10] [ 7%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] tests/test_binary.py::test_join[same] [gw2] [ 8%] FAILED tests/test_binary.py::test_nearest[upstream-True-opposite] tests/test_binary.py::test_nearest[upstream-False-False] [gw7] [ 8%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] [gw4] [ 8%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] [gw0] [ 8%] FAILED tests/test_binary.py::test_set_intersect[same] tests/test_binary.py::test_set_union[False] [gw9] [ 8%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] [gw10] [ 9%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] [gw1] [ 9%] FAILED tests/test_binary.py::test_coverage[opposite] tests/test_binary.py::test_subtraction[same] [gw6] [ 9%] FAILED tests/test_binary.py::test_k_nearest[upstream-True-False-last] tests/test_binary.py::test_k_nearest[None-False-opposite-last] [gw6] [ 9%] FAILED tests/test_binary.py::test_k_nearest[None-False-opposite-last] tests/test_binary.py::test_k_nearest[None-False-same-last] [gw7] [ 9%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] [gw5] [ 9%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] [gw2] [ 10%] FAILED tests/test_binary.py::test_nearest[upstream-False-False] tests/test_binary.py::test_nearest[upstream-False-same] [gw6] [ 10%] FAILED tests/test_binary.py::test_k_nearest[None-False-same-last] tests/test_binary.py::test_k_nearest[None-False-False-last] [gw8] [ 10%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] [gw4] [ 10%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] [gw10] [ 10%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] [gw2] [ 11%] FAILED tests/test_binary.py::test_nearest[upstream-False-same] tests/test_binary.py::test_nearest[upstream-False-opposite] [gw3] [ 11%] PASSED tests/test_binary.py::test_join[same] tests/test_binary.py::test_join[opposite] [gw9] [ 11%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] [gw5] [ 11%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] [gw4] [ 11%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain67-method_chain67] [gw6] [ 12%] FAILED tests/test_binary.py::test_k_nearest[None-False-False-last] tests/test_binary.py::test_k_nearest[None-True-opposite-last] [gw7] [ 12%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] [gw4] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain67-method_chain67] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] [gw2] [ 12%] FAILED tests/test_binary.py::test_nearest[upstream-False-opposite] tests/test_binary.py::test_nearest[downstream-True-False] [gw8] [ 12%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] [gw10] [ 12%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] [gw9] [ 13%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] [gw6] [ 13%] FAILED tests/test_binary.py::test_k_nearest[None-True-opposite-last] tests/test_binary.py::test_k_nearest[None-True-same-last] [gw5] [ 13%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] [gw6] [ 13%] FAILED tests/test_binary.py::test_k_nearest[None-True-same-last] tests/test_binary.py::test_k_nearest[None-True-False-last] [gw0] [ 13%] FAILED tests/test_binary.py::test_set_union[False] tests/test_binary.py::test_set_union[same] [gw1] [ 14%] FAILED tests/test_binary.py::test_subtraction[same] tests/test_binary.py::test_subtraction[opposite] [gw4] [ 14%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain69-method_chain69] [gw7] [ 14%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] [gw3] [ 14%] PASSED tests/test_binary.py::test_join[opposite] [gw10] [ 14%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] tests/test_binary.py::test_reldist [gw9] [ 15%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] [gw4] [ 15%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain69-method_chain69] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] [gw6] [ 15%] FAILED tests/test_binary.py::test_k_nearest[None-True-False-last] tests/test_binary.py::test_k_nearest_1_vs_nearest [gw7] [ 15%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] [gw10] [ 15%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] [gw9] [ 16%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] [gw5] [ 16%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] [gw2] [ 16%] FAILED tests/test_binary.py::test_nearest[downstream-True-False] tests/test_binary.py::test_nearest[downstream-True-same] [gw8] [ 16%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] [gw6] [ 16%] FAILED tests/test_binary.py::test_k_nearest_1_vs_nearest tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain93-method_chain93] [gw3] [ 16%] PASSED tests/test_binary.py::test_reldist tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] [gw7] [ 17%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] [gw6] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain93-method_chain93] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain94-method_chain94] [gw0] [ 17%] FAILED tests/test_binary.py::test_set_union[same] tests/test_binary.py::test_overlap[False] [gw6] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain94-method_chain94] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain95-method_chain95] [gw1] [ 17%] FAILED tests/test_binary.py::test_subtraction[opposite] tests/test_binary.py::test_subtraction[False] [gw5] [ 18%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain16-method_chain16] [gw10] [ 18%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain65-method_chain65] [gw6] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain95-method_chain95] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] [gw5] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain16-method_chain16] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] [gw10] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain65-method_chain65] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] [gw9] [ 19%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] [gw4] [ 19%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] [gw8] [ 19%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] [gw7] [ 19%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] [gw9] [ 19%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain79-method_chain79] [gw9] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain79-method_chain79] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] [gw6] [ 20%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain97-method_chain97] [gw6] [ 20%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain97-method_chain97] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] [gw7] [ 20%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] [gw2] [ 20%] FAILED tests/test_binary.py::test_nearest[downstream-True-same] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] tests/test_binary.py::test_nearest[downstream-True-opposite] [gw0] [ 20%] PASSED tests/test_binary.py::test_overlap[False] tests/test_binary.py::test_overlap[same] [gw3] [ 21%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] tests/test_binary.py::test_k_nearest[downstream-False-same-last] [gw1] [ 21%] FAILED tests/test_binary.py::test_subtraction[False] tests/test_binary.py::test_nearest[None-True-False] [gw7] [ 21%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] [gw6] [ 21%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] [gw3] [ 21%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-same-last] tests/test_binary.py::test_k_nearest[downstream-False-False-last] [gw5] [ 22%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain18-method_chain18] [gw10] [ 22%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] [gw5] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain18-method_chain18] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] [gw4] [ 22%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] [gw2] [ 22%] FAILED tests/test_binary.py::test_nearest[downstream-True-opposite] tests/test_binary.py::test_nearest[downstream-False-False] [gw8] [ 22%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] [gw0] [ 23%] PASSED tests/test_binary.py::test_overlap[same] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] tests/test_binary.py::test_overlap[opposite] [gw3] [ 23%] FAILED tests/test_binary.py::test_k_nearest[downstream-False-False-last] tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] [gw7] [ 23%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] [gw6] [ 23%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] [gw1] [ 23%] FAILED tests/test_binary.py::test_nearest[None-True-False] tests/test_binary.py::test_nearest[None-True-same] [gw9] [ 24%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain81-method_chain81] [gw9] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain81-method_chain81] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] [gw6] [ 24%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] [gw7] [ 24%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] [gw5] [ 24%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] [gw4] [ 25%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] [gw1] [ 25%] FAILED tests/test_binary.py::test_nearest[None-True-same] tests/test_binary.py::test_nearest[None-True-opposite] [gw2] [ 25%] FAILED tests/test_binary.py::test_nearest[downstream-False-False] tests/test_binary.py::test_nearest[downstream-False-same] [gw3] [ 25%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] tests/test_binary.py::test_k_nearest[downstream-True-same-last] [gw0] [ 25%] PASSED tests/test_binary.py::test_overlap[opposite] tests/test_binary.py::test_intersect[False] [gw9] [ 25%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] [gw6] [ 26%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] [gw2] [ 26%] FAILED tests/test_binary.py::test_nearest[downstream-False-same] tests/test_binary.py::test_nearest[downstream-False-opposite] [gw5] [ 26%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain83-method_chain83] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] [gw8] [ 26%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] [gw7] [ 26%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] [gw9] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain83-method_chain83] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] [gw1] [ 27%] FAILED tests/test_binary.py::test_nearest[None-True-opposite] tests/test_binary.py::test_nearest[None-False-False] [gw10] [ 27%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] [gw2] [ 27%] FAILED tests/test_binary.py::test_nearest[downstream-False-opposite] tests/test_binary.py::test_jaccard[False] [gw1] [ 27%] FAILED tests/test_binary.py::test_nearest[None-False-False] tests/test_binary.py::test_nearest[None-False-same] [gw6] [ 28%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] [gw1] [ 28%] FAILED tests/test_binary.py::test_nearest[None-False-same] tests/test_binary.py::test_nearest[None-False-opposite] [gw5] [ 28%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] [gw8] [ 28%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] [gw7] [ 28%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain114-method_chain114] [gw7] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain114-method_chain114] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] [gw4] [ 29%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] [gw9] [ 29%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] [gw0] [ 29%] PASSED tests/test_binary.py::test_intersect[False] tests/test_binary.py::test_intersect[same] [gw1] [ 29%] FAILED tests/test_binary.py::test_nearest[None-False-opposite] tests/test_binary.py::test_nearest[upstream-True-False] [gw6] [ 29%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] [gw5] [ 30%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] [gw8] [ 30%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain30-method_chain30] [gw3] [ 30%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-same-last] tests/test_binary.py::test_k_nearest[downstream-True-False-last] [gw8] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain30-method_chain30] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] [gw9] [ 30%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] [gw5] [ 31%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain142-method_chain142] [gw6] [ 31%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] [gw5] [ 31%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain142-method_chain142] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain143-method_chain143] [gw3] [ 31%] FAILED tests/test_binary.py::test_k_nearest[downstream-True-False-last] tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] [gw8] [ 31%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] [gw5] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain143-method_chain143] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain144-method_chain144] [gw2] [ 32%] FAILED tests/test_binary.py::test_jaccard[False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] [gw5] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain144-method_chain144] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] [gw10] [ 32%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] [gw0] [ 32%] PASSED tests/test_binary.py::test_intersect[same] tests/test_binary.py::test_intersect[opposite] [gw4] [ 32%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] [gw9] [ 33%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] [gw7] [ 33%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] [gw6] [ 33%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] [gw8] [ 33%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] [gw5] [ 33%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] [gw2] [ 34%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] [gw1] [ 34%] FAILED tests/test_binary.py::test_nearest[upstream-True-False] [gw3] [ 34%] FAILED tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain146-method_chain146] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain116-method_chain116] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain163-method_chain163] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain177-method_chain177] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] [gw7] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain116-method_chain116] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] [gw8] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain177-method_chain177] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain178-method_chain178] [gw5] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain146-method_chain146] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] [gw1] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain163-method_chain163] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] [gw8] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain178-method_chain178] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain179-method_chain179] [gw1] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain165-method_chain165] [gw8] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain179-method_chain179] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] [gw1] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain165-method_chain165] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] [gw0] [ 36%] PASSED tests/test_binary.py::test_intersect[opposite] [gw10] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] tests/test_binary.py::test_coverage[False] [gw3] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] [gw2] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] [gw9] [ 36%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] [gw6] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] [gw8] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain181-method_chain181] [gw7] [ 37%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain118-method_chain118] [gw8] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain181-method_chain181] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] [gw7] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain118-method_chain118] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] [gw5] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] [gw1] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain167-method_chain167] [gw4] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] [gw3] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] [gw1] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain167-method_chain167] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] [gw10] [ 38%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] [gw6] [ 39%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] [gw9] [ 39%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] [gw2] [ 39%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] [gw10] [ 39%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain128-method_chain128] [gw5] [ 39%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] [gw8] [ 40%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] [gw10] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain128-method_chain128] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain129-method_chain129] [gw10] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain129-method_chain129] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain130-method_chain130] [gw6] [ 40%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] [gw10] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain130-method_chain130] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] [gw9] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] [gw4] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] [gw2] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] [gw0] [ 41%] FAILED tests/test_binary.py::test_coverage[False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] [gw5] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] [gw6] [ 41%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] [gw8] [ 42%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] [gw3] [ 42%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] [gw10] [ 42%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain132-method_chain132] [gw7] [ 42%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] [gw10] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain132-method_chain132] [gw2] [ 43%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] [gw0] [ 43%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] [gw9] [ 43%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] [gw5] [ 43%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain230-method_chain230] [gw6] [ 43%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain212-method_chain212] [gw5] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain230-method_chain230] [gw8] [ 44%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] [gw6] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain212-method_chain212] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain213-method_chain213] [gw1] [ 44%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] [gw3] [ 44%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain191-method_chain191] [gw6] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain213-method_chain213] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain214-method_chain214] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] [gw6] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain214-method_chain214] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] [gw3] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain191-method_chain191] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] [gw9] [ 45%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] [gw0] [ 45%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] [gw2] [ 45%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] [gw10] [ 46%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] [gw6] [ 46%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain216-method_chain216] [gw5] [ 46%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] [gw6] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain216-method_chain216] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] [gw4] [ 46%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] [gw9] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] [gw8] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] [gw0] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] [gw2] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] [gw5] [ 47%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] [gw10] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] [gw2] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] [gw7] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] [gw9] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] [gw8] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] [gw0] [ 48%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] [gw1] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] [gw5] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] [gw10] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] [gw3] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain193-method_chain193] [gw2] [ 49%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] [gw3] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain193-method_chain193] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] [gw9] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain240-method_chain240] [gw8] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] [gw9] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain240-method_chain240] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain241-method_chain241] [gw0] [ 50%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] [gw9] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain241-method_chain241] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain242-method_chain242] [gw4] [ 51%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] [gw6] [ 51%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] [gw9] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain242-method_chain242] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] [gw3] [ 51%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain195-method_chain195] [gw3] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain195-method_chain195] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] [gw8] [ 52%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] [gw2] [ 52%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] [gw1] [ 52%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] [gw0] [ 52%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] [gw7] [ 52%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] [gw9] [ 53%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain244-method_chain244] [gw5] [ 53%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] [gw10] [ 53%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] [gw8] [ 53%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] [gw9] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain244-method_chain244] [gw2] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] [gw3] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] [gw0] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] [gw4] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] [gw5] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] [gw1] [ 54%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] [gw10] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] [gw8] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] [gw0] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] [gw9] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] [gw3] [ 55%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] [gw2] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] [gw6] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] [gw7] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain263-method_chain263] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] [gw10] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] [gw5] [ 56%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] [gw6] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain263-method_chain263] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] [gw8] [ 57%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] [gw0] [ 57%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] [gw9] [ 57%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] [gw3] [ 57%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain279-method_chain279] [gw1] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] [gw3] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain279-method_chain279] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] [gw2] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] [gw10] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] [gw6] [ 58%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain265-method_chain265] [gw6] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain265-method_chain265] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] [gw5] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] [gw8] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] [gw0] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] [gw9] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] [gw4] [ 59%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] [gw2] [ 60%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain293-method_chain293] [gw10] [ 60%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] [gw2] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain293-method_chain293] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] [gw3] [ 60%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] [gw9] [ 60%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] [gw8] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] [gw1] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] [gw5] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] [gw0] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] [gw7] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] [gw10] [ 61%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] [gw3] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] [gw8] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain310-method_chain310] [gw2] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] [gw9] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] [gw4] [ 62%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] [gw8] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain310-method_chain310] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] [gw0] [ 63%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] [gw5] [ 63%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] [gw10] [ 63%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain261-method_chain261] [gw10] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain261-method_chain261] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] [gw4] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] [gw9] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain289-method_chain289] [gw10] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] [gw3] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] [gw6] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] [gw2] [ 64%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] [gw0] [ 65%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] [gw9] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain289-method_chain289] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain290-method_chain290] [gw8] [ 65%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain312-method_chain312] [gw8] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain312-method_chain312] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] [gw5] [ 65%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] [gw1] [ 66%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] [gw4] [ 66%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain226-method_chain226] [gw4] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain226-method_chain226] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain227-method_chain227] [gw2] [ 66%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] [gw4] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain227-method_chain227] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain228-method_chain228] [gw0] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] [gw10] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] [gw5] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] [gw7] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] [gw4] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain228-method_chain228] [gw8] [ 67%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain331-method_chain331] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain314-method_chain314] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] [gw8] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain314-method_chain314] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] [gw2] [ 68%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain326-method_chain326] [gw2] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain326-method_chain326] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] [gw3] [ 68%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] [gw0] [ 68%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] [gw10] [ 69%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] [gw4] [ 69%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain331-method_chain331] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain332-method_chain332] [gw5] [ 69%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] [gw7] [ 69%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] [gw6] [ 69%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] [gw9] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain290-method_chain290] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain291-method_chain291] [gw3] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain340-method_chain340] [gw2] [ 70%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain328-method_chain328] [gw9] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain291-method_chain291] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain348-method_chain348] [gw3] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain340-method_chain340] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] [gw2] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain328-method_chain328] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] [gw7] [ 71%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain275-method_chain275] [gw0] [ 71%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] [gw5] [ 71%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain344-method_chain344] [gw10] [ 71%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain324-method_chain324] [gw7] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain275-method_chain275] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] [gw1] [ 72%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] [gw7] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain277-method_chain277] [gw10] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain324-method_chain324] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] [gw7] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain277-method_chain277] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] [gw3] [ 72%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] [gw8] [ 73%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain342-method_chain342] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain336-method_chain336] [gw3] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain342-method_chain342] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain343-method_chain343] [gw9] [ 73%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain348-method_chain348] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] [gw6] [ 73%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] [gw0] [ 73%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] [gw5] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain344-method_chain344] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain345-method_chain345] [gw7] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain357-method_chain357] [gw2] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain330-method_chain330] [gw8] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain336-method_chain336] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] [gw10] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain360-method_chain360] [gw9] [ 74%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain350-method_chain350] [gw4] [ 75%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain332-method_chain332] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain333-method_chain333] [gw0] [ 75%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] [gw3] [ 75%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain343-method_chain343] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain363-method_chain363] [gw3] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain363-method_chain363] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain364-method_chain364] [gw8] [ 75%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] [gw5] [ 76%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain345-method_chain345] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain338-method_chain338] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain346-method_chain346] [gw8] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain338-method_chain338] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain339-method_chain339] [gw2] [ 76%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain330-method_chain330] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] [gw8] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain339-method_chain339] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain369-method_chain369] [gw4] [ 76%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain333-method_chain333] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain334-method_chain334] [gw7] [ 77%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain357-method_chain357] [gw0] [ 77%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] [gw9] [ 77%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain350-method_chain350] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain351-method_chain351] [gw1] [ 77%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] [gw6] [ 77%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] [gw4] [ 77%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain334-method_chain334] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain335-method_chain335] [gw7] [ 78%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain359-method_chain359] [gw5] [ 78%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain346-method_chain346] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain347-method_chain347] [gw0] [ 78%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] [gw7] [ 78%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain359-method_chain359] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain381-method_chain381] [gw9] [ 78%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain351-method_chain351] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain372-method_chain372] [gw1] [ 79%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] [gw2] [ 79%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] [gw4] [ 79%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain335-method_chain335] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] [gw10] [ 79%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain360-method_chain360] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain361-method_chain361] [gw5] [ 79%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain347-method_chain347] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain383-method_chain383] [gw9] [ 80%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain372-method_chain372] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain373-method_chain373] [gw10] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain361-method_chain361] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain362-method_chain362] [gw9] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain373-method_chain373] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain374-method_chain374] [gw0] [ 80%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain385-method_chain385] [gw8] [ 80%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain369-method_chain369] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain370-method_chain370] [gw3] [ 80%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain364-method_chain364] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] [gw5] [ 81%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain383-method_chain383] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain384-method_chain384] [gw6] [ 81%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain375-method_chain375] [gw7] [ 81%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain381-method_chain381] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain382-method_chain382] [gw6] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain375-method_chain375] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain376-method_chain376] [gw4] [ 81%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] [gw1] [ 82%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] [gw0] [ 82%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain385-method_chain385] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain386-method_chain386] [gw10] [ 82%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain362-method_chain362] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain387-method_chain387] [gw10] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain387-method_chain387] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] [gw2] [ 82%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] [gw5] [ 83%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain384-method_chain384] [gw7] [ 83%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain382-method_chain382] [gw8] [ 83%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain370-method_chain370] [gw4] [ 83%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] [gw6] [ 83%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain376-method_chain376] [gw0] [ 83%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain386-method_chain386] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain393-method_chain393] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain399-method_chain399] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain377-method_chain377] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain395-method_chain395] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain380-method_chain380] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain371-method_chain371] [gw3] [ 84%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain391-method_chain391] [gw6] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain377-method_chain377] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain403-method_chain403] [gw3] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain391-method_chain391] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain392-method_chain392] [gw9] [ 84%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain374-method_chain374] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain389-method_chain389] [gw9] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain389-method_chain389] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain390-method_chain390] [gw4] [ 85%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain380-method_chain380] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] [gw7] [ 85%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain395-method_chain395] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain396-method_chain396] [gw8] [ 85%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain371-method_chain371] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain404-method_chain404] [gw0] [ 85%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain399-method_chain399] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain400-method_chain400] [gw1] [ 85%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] [gw5] [ 86%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain393-method_chain393] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain394-method_chain394] [gw6] [ 86%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain403-method_chain403] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain406-method_chain406] [gw3] [ 86%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain392-method_chain392] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain407-method_chain407] [gw4] [ 86%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain409-method_chain409] [gw9] [ 86%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain390-method_chain390] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain408-method_chain408] [gw10] [ 87%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain401-method_chain401] [gw2] [ 87%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] [gw9] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain408-method_chain408] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain417-method_chain417] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain402-method_chain402] [gw7] [ 87%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain396-method_chain396] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain410-method_chain410] [gw8] [ 87%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain404-method_chain404] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] [gw7] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain410-method_chain410] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] [gw5] [ 88%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain394-method_chain394] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain413-method_chain413] [gw3] [ 88%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain407-method_chain407] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain415-method_chain415] [gw0] [ 88%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain400-method_chain400] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain412-method_chain412] [gw1] [ 88%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain398-method_chain398] [gw0] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain412-method_chain412] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain426-method_chain426] [gw6] [ 89%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain406-method_chain406] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain414-method_chain414] [gw10] [ 89%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain401-method_chain401] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain418-method_chain418] [gw2] [ 89%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain402-method_chain402] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] [gw8] [ 89%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain422-method_chain422] [gw0] [ 89%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain426-method_chain426] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] [gw8] [ 90%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain422-method_chain422] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain432-method_chain432] [gw7] [ 90%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain423-method_chain423] [gw1] [ 90%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain398-method_chain398] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain427-method_chain427] [gw2] [ 90%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] [gw8] [ 90%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain432-method_chain432] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] [gw0] [ 90%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] [gw4] [ 91%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain409-method_chain409] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] [gw9] [ 91%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain417-method_chain417] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] [gw3] [ 91%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain415-method_chain415] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] [gw2] [ 91%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain437-method_chain437] [gw1] [ 91%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain427-method_chain427] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain436-method_chain436] [gw1] [ 92%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain436-method_chain436] tests/test_getset_attr.py::test_getsetattr_with_str [gw1] [ 92%] PASSED tests/test_getset_attr.py::test_getsetattr_with_str tests/test_io.py::test_read_gtf [gw1] [ 92%] PASSED tests/test_io.py::test_read_gtf tests/test_io.py::test_read_gff3 [gw1] [ 92%] PASSED tests/test_io.py::test_read_gff3 tests/test_io.py::test_read_bed [gw1] [ 92%] PASSED tests/test_io.py::test_read_bed tests/test_pickle.py::test_pickle [gw1] [ 93%] PASSED tests/test_pickle.py::test_pickle tests/test_stranded.py::test_stranded [gw1] [ 93%] PASSED tests/test_stranded.py::test_stranded tests/test_stranded.py::test_unstrand [gw1] [ 93%] PASSED tests/test_stranded.py::test_unstrand tests/test_unary.py::test_merge[True] [gw0] [ 93%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] [gw5] [ 93%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain413-method_chain413] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain424-method_chain424] [gw5] [ 93%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain424-method_chain424] tests/test_unary.py::test_cluster[False] [gw8] [ 94%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain438-method_chain438] [gw6] [ 94%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain414-method_chain414] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] [gw1] [ 94%] FAILED tests/test_unary.py::test_merge[True] tests/test_unary.py::test_merge[False] [gw8] [ 94%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain438-method_chain438] tests/test_unary.py::test_cluster_by[False] [gw3] [ 94%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] tests/test_getset_attr.py::test_getsetattr [gw3] [ 95%] PASSED tests/test_getset_attr.py::test_getsetattr tests/test_unary.py::test_init[True] [gw10] [ 95%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain418-method_chain418] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] [gw4] [ 95%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain440-method_chain440] [gw5] [ 95%] FAILED tests/test_unary.py::test_cluster[False] tests/test_unary.py::test_cluster_by[True] [gw4] [ 95%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain440-method_chain440] tests/test_unary.py::test_summary [gw0] [ 96%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] tests/test_unary.py::test_cluster[True] [gw1] [ 96%] FAILED tests/test_unary.py::test_merge[False] tests/test_unary.py::test_merge_by[False] [gw3] [ 96%] PASSED tests/test_unary.py::test_init[True] tests/test_unary.py::test_init[False] [gw4] [ 96%] FAILED tests/test_unary.py::test_summary tests/windows/test_windows.py::test_windows2 [gw6] [ 96%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] [gw4] [ 96%] FAILED tests/windows/test_windows.py::test_windows2 tests/test_unary.py::test_merge_by[True] [gw7] [ 97%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain423-method_chain423] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] [gw3] [ 97%] PASSED tests/test_unary.py::test_init[False] [gw9] [ 97%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] tests/test_genomicfeatures.py::test_introns_single [gw9] [ 97%] FAILED tests/test_genomicfeatures.py::test_introns_single [gw0] [ 97%] FAILED tests/test_unary.py::test_cluster[True] [gw10] [ 98%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] tests/test_unary.py::test_getitem [gw7] [ 98%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] [gw2] [ 98%] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain437-method_chain437] tests/test_getset_attr.py::test_getsetattr_fails [gw2] [ 98%] PASSED tests/test_getset_attr.py::test_getsetattr_fails [gw10] [ 98%] PASSED tests/test_unary.py::test_getitem [gw1] [ 99%] PASSED tests/test_unary.py::test_merge_by[False] [gw6] [ 99%] PASSED tests/test_unary.py::test_merge_by[True] [gw5] [ 99%] PASSED tests/test_unary.py::test_cluster_by[True] tests/windows/test_windows.py::test_windows [gw5] [ 99%] FAILED tests/windows/test_windows.py::test_windows [gw8] [ 99%] PASSED tests/test_unary.py::test_cluster_by[False] tests/test_unary.py::test_windows [gw8] [100%] FAILED tests/test_unary.py::test_windows =================================== FAILURES =================================== ___________________ test_k_nearest[upstream-False-same-last] ___________________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1e.values, d2s.values, d1e.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=False, | strandedness='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 41 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGDFEADi2Axc=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1s.values, d2e.values, d1s.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=False, | strandedness='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6lxg9la3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6lxg9la3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpceg6hkn3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpceg6hkn3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps0ozmmls/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps0ozmmls/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfnv2obp0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfnv2obp0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqi90ais8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqi90ais8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpizfxy0h_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpizfxy0h_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf9901few/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf9901few/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnr3xhfmq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnr3xhfmq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp36ijdq5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36ijdq5a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwsgsnjzy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwsgsnjzy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp69bjwraj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp69bjwraj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvqi4se6e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvqi4se6e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmponsbv4v2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmponsbv4v2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx0fphnhb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx0fphnhb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6fu5extx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6fu5extx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaxqyn5h2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaxqyn5h2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_i7f1zun/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_i7f1zun/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpayijke3z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpayijke3z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp54qyq4rq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp54qyq4rq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprtv8okti/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprtv8okti/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6d5u277v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6d5u277v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg9ax7s86/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg9ax7s86/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmv48igie/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmv48igie/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk3bxul15/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk3bxul15/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4kmn7gpm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4kmn7gpm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp602g9_ko/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp602g9_ko/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpel554j28/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpel554j28/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3tz1yw27/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3tz1yw27/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbhkbxgxq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbhkbxgxq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2wnwam_g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2wnwam_g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdjsdnxz4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdjsdnxz4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzyz03r75/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzyz03r75/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1hy4x2gz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1hy4x2gz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdzknpddx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdzknpddx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph9nl7hp8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph9nl7hp8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptpalxc5t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptpalxc5t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg1j7ligq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg1j7ligq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy5e09_eq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy5e09_eq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn07awcf8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn07awcf8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphxvqt908/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphxvqt908/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcg_cfppa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcg_cfppa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpngg5rcwg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpngg5rcwg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0r2m37mc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0r2m37mc/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain19-method_chain19] ___________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 109 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr14 | 6207059 | 6212437 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr14 | 6207059 | 6212437 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ___________ test_three_in_a_row[strandedness_chain55-method_chain55] ___________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 183 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ____________ test_three_in_a_row[strandedness_chain0-method_chain0] ____________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 241 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ____________ test_three_in_a_row[strandedness_chain7-method_chain7] ____________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 124 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ___________ test_three_in_a_row[strandedness_chain31-method_chain31] ___________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIMORCchghIkwOoIEwOJQQUYYYgAAgvgEow==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ___________ test_three_in_a_row[strandedness_chain43-method_chain43] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain56-method_chain56] ___________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 115 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________________ test_k_nearest[upstream-False-False-last] ___________________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1e.values, d2s.values, d1e.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=False, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:42 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:46 | (and 38 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGMEijDDEAAAx1ALW') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1s.values, d2e.values, d1s.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=False, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:19 | (and 36 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl3px2m31/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl3px2m31/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbikxzmhj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbikxzmhj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcedepwgf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcedepwgf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1wgjtbed/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1wgjtbed/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj2k7qemg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj2k7qemg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpget990nw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpget990nw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq8ti4s2q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq8ti4s2q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9iyi1j3q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9iyi1j3q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb6e8i46h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb6e8i46h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu3o10vm6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu3o10vm6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpncmxzdgj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpncmxzdgj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6knyq369/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6knyq369/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbc8dpq2m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbc8dpq2m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz972t3r4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz972t3r4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2hkbvvwf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2hkbvvwf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp03jcmtut/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp03jcmtut/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpio6gdvaj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpio6gdvaj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6vihn91p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6vihn91p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjwk66el3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjwk66el3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp87rkneoi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp87rkneoi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuczk3khv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuczk3khv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpork5qi5f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpork5qi5f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy4gtao6p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy4gtao6p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3tno2n_m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3tno2n_m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnyqdrw0k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnyqdrw0k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi5j44642/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi5j44642/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1gcoen0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1gcoen0e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphsrr8l49/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphsrr8l49/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp46bfjli9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp46bfjli9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz4yqyxs1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz4yqyxs1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpip8atal4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpip8atal4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaj4y0ec9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaj4y0ec9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp529oglka/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp529oglka/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppwsh9yw3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppwsh9yw3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb3nfn2f5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb3nfn2f5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7x8yjpch/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7x8yjpch/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0ap7u3l8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ap7u3l8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1xlt0l1e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1xlt0l1e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu9w8uusf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu9w8uusf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp84c1p0d9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp84c1p0d9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphxivx4ag/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphxivx4ag/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfbt03ljh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfbt03ljh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo22fet5v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo22fet5v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx6y8yr6f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx6y8yr6f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm_wflng5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm_wflng5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphzlbv_a1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphzlbv_a1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp0pemxr3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp0pemxr3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpabx4o79c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpabx4o79c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzgvbgchk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzgvbgchk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2kk_8pwr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2kk_8pwr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp74rjo_wk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp74rjo_wk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpapo3j8ei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpapo3j8ei/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppyoxsdlb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppyoxsdlb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaq8gyd6v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaq8gyd6v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpktaz8mqm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpktaz8mqm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy2f1uez1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy2f1uez1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzvi_q0eo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzvi_q0eo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp979x38lh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp979x38lh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsdogopx6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsdogopx6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv50fd2mf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv50fd2mf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgc8lbw9y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgc8lbw9y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0zbcs8ah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0zbcs8ah/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq570wp7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq570wp7q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsavnf61g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsavnf61g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyst360q1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyst360q1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy9f8ekrg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy9f8ekrg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp75_1v7kn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp75_1v7kn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd0p63djt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd0p63djt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8tezz9nr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8tezz9nr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9mno26g0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9mno26g0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_o8_50cu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_o8_50cu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprcbridir/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprcbridir/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgexyb_ll/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgexyb_ll/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm20x26gw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm20x26gw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx4qqtpib/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx4qqtpib/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz57px0rm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz57px0rm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpocu_b9nl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpocu_b9nl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxxijjbjo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxxijjbjo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkx5jgran/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkx5jgran/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbowensmx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbowensmx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm09ayccl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm09ayccl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmptvy7bm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmptvy7bm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbq1cwmct/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbq1cwmct/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwed8iiks/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwed8iiks/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx3rgg1bb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3rgg1bb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplpnhwnce/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplpnhwnce/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdmv8jrw6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdmv8jrw6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplul_99o0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplul_99o0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe__udtl_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe__udtl_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6iarhci3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6iarhci3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu5gap52c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu5gap52c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzr61demu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzr61demu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvytjy70o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvytjy70o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp4v2m10u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp4v2m10u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb5g41dp0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb5g41dp0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5oj3k9q_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5oj3k9q_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_h7hj3o9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_h7hj3o9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdkl40djr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdkl40djr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpot_hjbrm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpot_hjbrm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn5lmom1s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn5lmom1s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpao_cn38u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpao_cn38u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpixs_m7ar/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpixs_m7ar/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpztldhlic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpztldhlic/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv32hz0fb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv32hz0fb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpowki1g8c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpowki1g8c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_63uv0sv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_63uv0sv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpix0yq136/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpix0yq136/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvmeyz00n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvmeyz00n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0_k7dqp4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_k7dqp4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgi5a13fk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgi5a13fk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn2b2hl8v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn2b2hl8v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9hrf5a96/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9hrf5a96/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwbxcdnow/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwbxcdnow/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp39xzrwvi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp39xzrwvi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptrwsjnjr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptrwsjnjr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi740deik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi740deik/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8bnj_zz6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8bnj_zz6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpisxnv7va/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpisxnv7va/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppt2r8jo_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppt2r8jo_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp17hi0se2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp17hi0se2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpofiqnt7l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpofiqnt7l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpka5eex0_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpka5eex0_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvrw9lj3p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvrw9lj3p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph81cv2yv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph81cv2yv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp068k5efu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp068k5efu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7_eo6vz8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7_eo6vz8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplncfy8hu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplncfy8hu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1ugwckld/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ugwckld/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkq9j7pho/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkq9j7pho/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphidmytb1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphidmytb1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4unrxikp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4unrxikp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx_qxfmn9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx_qxfmn9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2qlx4cs5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2qlx4cs5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2pg7w2zh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2pg7w2zh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnoru1v9h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnoru1v9h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpva1qlxsv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpva1qlxsv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2inzu8s2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2inzu8s2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv1py2xno/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv1py2xno/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd9yy80_l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd9yy80_l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzy8a3jar/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzy8a3jar/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmposjhx9bu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmposjhx9bu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm39ladxs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm39ladxs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnz7izy8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnz7izy8_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4re6m3wz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4re6m3wz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphbht81gz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphbht81gz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0a3mq594/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0a3mq594/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc8uz66dc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc8uz66dc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsgo7brz2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsgo7brz2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3iziwehi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3iziwehi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0_ppv2tt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_ppv2tt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7lg13j5h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7lg13j5h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3js2oso0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3js2oso0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3t05hhxk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3t05hhxk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkwup2aty/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkwup2aty/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdzk50hby/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdzk50hby/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvz6tx46m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvz6tx46m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyi455c4a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyi455c4a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc5b6n4hg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc5b6n4hg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ejhgjy2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ejhgjy2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpavqclhb_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpavqclhb_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk7bl6408/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk7bl6408/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvleuwxyh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvleuwxyh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0jvmhrux/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0jvmhrux/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi34lxpx2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi34lxpx2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkr8900in/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkr8900in/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5giivnsn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5giivnsn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyn7rpcdn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyn7rpcdn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9v4dluc5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9v4dluc5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcjm86x4x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcjm86x4x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqnrhjwq9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqnrhjwq9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvovdceld/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvovdceld/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq5la58_1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq5la58_1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmptzlt0o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmptzlt0o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp514f91dp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp514f91dp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqcs_jsu2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqcs_jsu2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpycv0lb52/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpycv0lb52/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzje6a1c3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzje6a1c3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8zisb1nx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8zisb1nx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg5cjsbkx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg5cjsbkx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxojnsv7l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxojnsv7l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1sp32onv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1sp32onv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsklyckey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsklyckey/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuogyugym/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuogyugym/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdd8yu6bk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdd8yu6bk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo2q44hgz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo2q44hgz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf2ss5ann/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf2ss5ann/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcsu0r5wu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcsu0r5wu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpybfdrx0k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpybfdrx0k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppe7ga_td/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppe7ga_td/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgariyy39/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgariyy39/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1gags8rj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1gags8rj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq72uoiw7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq72uoiw7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwh3h4cpl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwh3h4cpl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo8hl0km5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo8hl0km5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpflr1zj71/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpflr1zj71/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpldd4laot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpldd4laot/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3t0y7a7l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3t0y7a7l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp00nkwseh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00nkwseh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp65rik4pv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp65rik4pv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzp_ur7xj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzp_ur7xj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphwc5yt9l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphwc5yt9l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqpdvclpo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqpdvclpo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp1f_hfa1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp1f_hfa1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5ruauedl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ruauedl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgf4o449f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgf4o449f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg2nl1mcm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg2nl1mcm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm03e4qeg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm03e4qeg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk9528tzr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk9528tzr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplei9dpik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplei9dpik/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2fi294yx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2fi294yx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqc34uv8q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqc34uv8q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjpcczlts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjpcczlts/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl22lzdwd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl22lzdwd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuaezd7ns/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuaezd7ns/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvsh81awm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvsh81awm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsbgqu2t8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsbgqu2t8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpedd6ahgn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpedd6ahgn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0asbbzog/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0asbbzog/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeqbje0ia/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeqbje0ia/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9lyy2fan/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9lyy2fan/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy1uc_3b2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy1uc_3b2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwgrl8xb2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwgrl8xb2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjfgssn2p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjfgssn2p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdm_r4839/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdm_r4839/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdl3n4y94/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdl3n4y94/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1sdytpht/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1sdytpht/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl9pz0bnw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl9pz0bnw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8qjcnb4z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8qjcnb4z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ywqfm3e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ywqfm3e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpswd5tbrz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpswd5tbrz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps3yd_wz5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps3yd_wz5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpth2xkv8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpth2xkv8_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_952upvl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_952upvl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeo8djj2l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeo8djj2l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbjp4zy0w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbjp4zy0w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqn1zpl0v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqn1zpl0v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo6txa9lw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo6txa9lw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr79331g8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr79331g8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4691yv6q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4691yv6q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwvsa69p_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwvsa69p_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8e31szej/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8e31szej/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp65xyz1rm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp65xyz1rm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpin6yzjm9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpin6yzjm9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwwz69sg4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwwz69sg4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8p6q0xec/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8p6q0xec/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnt_h2_bt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnt_h2_bt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5k6rzima/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5k6rzima/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp3m4cjts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp3m4cjts/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb4ltx1ed/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb4ltx1ed/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjv__19d8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjv__19d8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcjvc0rjs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcjvc0rjs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6piopwd6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6piopwd6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfs2uqb_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfs2uqb_x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6i2xxle6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6i2xxle6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptg78g00l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptg78g00l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6ywn3rva/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ywn3rva/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgifatyr3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgifatyr3/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ______________________________ test_jaccard[same] ______________________________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:363: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:378: in test_jaccard result = gr.stats.jaccard(gr2, strandedness=strandedness) pyranges/statistics.py:766: in jaccard for v in self.set_intersect(other).lengths(as_dict=True).values()) pyranges/pyranges.py:3687: in set_intersect self_clusters = self.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_jaccard( E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3T2FW1mYHBkhCEGRiCJzAcARicDew==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ____________ test_three_in_a_row[strandedness_chain8-method_chain8] ____________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E (and 104 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain33-method_chain33] ___________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 105 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ____________ test_three_in_a_row[strandedness_chain1-method_chain1] ____________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/init.py:174 E (and 186 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________________________ test_set_intersect[False] ___________________________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:113: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:128: in test_set_intersect result = gr.set_intersect(gr2, strandedness=strandedness) pyranges/pyranges.py:3687: in set_intersect self_clusters = self.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_set_intersect( E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3QullBiYHBkhCEGRiCJzAcAP+YDQw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpl45lh13_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpl45lh13_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdumexvd1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdumexvd1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2rqg82sm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2rqg82sm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpo6n_dhgl/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo6n_dhgl/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpq57b4ibf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpq57b4ibf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpx8q1g9c0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx8q1g9c0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpp3s8u6gs/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp3s8u6gs/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9qjew89j/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9qjew89j/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpsod92xna/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsod92xna/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvexz0v6e/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvexz0v6e/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp26d412za/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp26d412za/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5l8y75ox/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5l8y75ox/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzci1cotw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzci1cotw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmps91svzxp/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps91svzxp/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpra3dunsk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpra3dunsk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbc8orfn4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbc8orfn4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp84k3vlgq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp84k3vlgq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpamt_fdgo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpamt_fdgo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmps963pd_6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps963pd_6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpyhjm6ivi/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyhjm6ivi/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpkplh0ske/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkplh0ske/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9ei5ft14/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9ei5ft14/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4ml17xcp/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4ml17xcp/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpu7icg9dv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu7icg9dv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpon7hdtzk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpon7hdtzk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcf0cbgod/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcf0cbgod/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnc2mgn4c/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnc2mgn4c/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpag548yno/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpag548yno/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxpgpv388/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxpgpv388/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpi49s7mrt/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi49s7mrt/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpp9qp8uwn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp9qp8uwn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpv60nqw51/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpv60nqw51/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpys26n5lc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpys26n5lc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpz3sxrc9f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpz3sxrc9f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpimiw_heb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpimiw_heb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3ks0vjec/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3ks0vjec/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp56o4w9gs/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp56o4w9gs/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6rj4pd6e/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6rj4pd6e/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_y_my1hv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_y_my1hv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqus6_sqn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqus6_sqn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6gml56o2/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6gml56o2/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7ex5060m/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7ex5060m/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2_uehm8q/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2_uehm8q/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdyern2vj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdyern2vj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp18t6n3gv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp18t6n3gv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpj0p5yoad/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpj0p5yoad/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgp3kfeeo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgp3kfeeo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzuw45_4c/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzuw45_4c/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpryzstskv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpryzstskv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpp8tu73p0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp8tu73p0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpixtsixe6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpixtsixe6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8xbby_qm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8xbby_qm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6uewfmx5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6uewfmx5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6q7atowr/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6q7atowr/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9kkrh6u1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9kkrh6u1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppxvm5krt/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppxvm5krt/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0_dsrmtj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0_dsrmtj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnvnv70vj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnvnv70vj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_h0fykn2/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_h0fykn2/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpisf2ceuo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpisf2ceuo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8r8d6doy/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8r8d6doy/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9t6kkoxv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9t6kkoxv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpx1r09d7l/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx1r09d7l/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphevtee48/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphevtee48/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpirnd4b4s/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpirnd4b4s/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp33bv2795/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp33bv2795/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprt8gklbk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprt8gklbk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwuvp5n6f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwuvp5n6f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppptfxctg/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppptfxctg/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvszb256t/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvszb256t/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgh3ku8m6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgh3ku8m6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnbhs55n4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnbhs55n4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpih8_a7w_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpih8_a7w_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5m_dqdc6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5m_dqdc6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpf24xfok5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf24xfok5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8abyn00_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8abyn00_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnt6spa8_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnt6spa8_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphlabifeu/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphlabifeu/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpm4p0qzyq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm4p0qzyq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpi6dj0hbf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi6dj0hbf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzdbemd5r/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzdbemd5r/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7clwdmzv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7clwdmzv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpp63olb5y/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp63olb5y/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvsz21sqk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvsz21sqk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1x16dtx0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1x16dtx0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjjde78hw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjjde78hw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9skir3pp/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9skir3pp/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpe1fosofk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe1fosofk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpf_te3yfo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf_te3yfo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpe4r4ilfn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe4r4ilfn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpmmz4rog3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmmz4rog3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3lhq6tm6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3lhq6tm6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpv6nrv6xm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpv6nrv6xm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp77_cbq3g/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp77_cbq3g/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5hml948k/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5hml948k/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcme8yzt1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcme8yzt1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3bmtcwri/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3bmtcwri/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpn4v0yihj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpn4v0yihj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqxvfhsh_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqxvfhsh_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzawrtm5c/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzawrtm5c/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_3s8wcwx/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_3s8wcwx/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpipuhdc6l/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpipuhdc6l/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpp7vt5upw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp7vt5upw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwbngwjni/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwbngwjni/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9s9f3ien/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9s9f3ien/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmplbw89gjw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplbw89gjw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprkpz8tqe/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprkpz8tqe/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5hq2_1sf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5hq2_1sf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1tuyri4m/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1tuyri4m/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5q7a6wpu/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5q7a6wpu/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbd3_wzwi/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbd3_wzwi/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnk9m_2jc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnk9m_2jc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpsdola0qk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsdola0qk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4rfswvvg/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4rfswvvg/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9kfe98mn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9kfe98mn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp47d5g8m1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp47d5g8m1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp81dzztry/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp81dzztry/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7gz9hy1s/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7gz9hy1s/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1g9tzi22/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1g9tzi22/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpc4c7nhl4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpc4c7nhl4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpkp6a4nyk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkp6a4nyk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7ks8zhn1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7ks8zhn1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpivyxz7dy/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpivyxz7dy/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp21udxhyw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp21udxhyw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpk35qb6p0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk35qb6p0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpfkocimmv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfkocimmv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpk8_566s0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk8_566s0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0a8_kt0z/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0a8_kt0z/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0p7qk0gy/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0p7qk0gy/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphiwvmg0l/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphiwvmg0l/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpycpdrk7v/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpycpdrk7v/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7wy7w7ok/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7wy7w7ok/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpt1er7jsa/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpt1er7jsa/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpiexxvsu3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpiexxvsu3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9viogne0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9viogne0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpr71oqsa6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpr71oqsa6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp11e6b_uh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp11e6b_uh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjqs4b0yo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjqs4b0yo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwdsfu0sm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwdsfu0sm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppqffxjy5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppqffxjy5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_bg2lbex/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_bg2lbex/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdzomnosz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdzomnosz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmph163bbww/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph163bbww/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6d1aqzsy/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6d1aqzsy/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpje6dwlzt/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpje6dwlzt/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpo9v5jqbv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo9v5jqbv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0zxgocco/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0zxgocco/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpntqtka92/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpntqtka92/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9zpzi8qo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9zpzi8qo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpss762iz7/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpss762iz7/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpb2rrfuq7/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpb2rrfuq7/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpso5f9fhw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpso5f9fhw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvqtoty6z/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvqtoty6z/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpl9c1b23q/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpl9c1b23q/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmptzu2wy_y/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptzu2wy_y/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpfmtllolz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfmtllolz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3gddc36w/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3gddc36w/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4b6w_1i1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4b6w_1i1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp5o_7wm9o/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5o_7wm9o/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpkieldoum/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkieldoum/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcyykmf5f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcyykmf5f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnv26xac4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnv26xac4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4bg0fz5v/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4bg0fz5v/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpp1dh995a/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp1dh995a/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcb2toum0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcb2toum0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_y8a7545/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_y8a7545/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpru_gfsis/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpru_gfsis/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp67uxxd1n/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp67uxxd1n/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpg_4378j1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpg_4378j1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnsnfh_5c/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnsnfh_5c/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpylar18if/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpylar18if/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0kvkucvc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0kvkucvc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp84ibb8f_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp84ibb8f_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpltywe5wd/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpltywe5wd/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwfod3oht/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwfod3oht/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3s2fnws9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3s2fnws9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpz3_fwrsc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpz3_fwrsc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcnqas4mv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcnqas4mv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmplr6o1blh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplr6o1blh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7rj1v0c0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7rj1v0c0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpes1tawj0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpes1tawj0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmptesu572z/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptesu572z/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpmumc1vky/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmumc1vky/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpksfl7ta7/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpksfl7ta7/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpq0xlf_rz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpq0xlf_rz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpngg04qzg/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpngg04qzg/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpoqsth9hf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpoqsth9hf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpubdingee/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpubdingee/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcmt0pwho/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcmt0pwho/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprgg9ogpq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprgg9ogpq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqchfv_ry/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqchfv_ry/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpeep5l0qg/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpeep5l0qg/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpukf7cddb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpukf7cddb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmptznmt68n/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptznmt68n/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxe6lmwnj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxe6lmwnj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppmo4l5w5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppmo4l5w5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_d3n0n4r/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_d3n0n4r/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpepjo5dzh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpepjo5dzh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpp_0nyfpm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp_0nyfpm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwljk7ri1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwljk7ri1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3ed4jpng/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3ed4jpng/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxg_397s0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxg_397s0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgbwe0cmk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgbwe0cmk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpplly69gh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpplly69gh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8_r1nd2n/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8_r1nd2n/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgiambpp4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgiambpp4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1mzqy4ll/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1mzqy4ll/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpx7y_mvj4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx7y_mvj4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_i14qcth/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_i14qcth/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcucqcr9e/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcucqcr9e/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8943od9b/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8943od9b/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpm802u55j/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm802u55j/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp30a17dho/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp30a17dho/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphj7tl6in/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphj7tl6in/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpfndbdgv_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfndbdgv_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6wqjgpqh/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6wqjgpqh/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp41dkk9m_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp41dkk9m_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6n89kjb0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6n89kjb0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpu_ydvvs1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu_ydvvs1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgtsy52i3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgtsy52i3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpmiwybt0c/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmiwybt0c/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_nagqpo3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_nagqpo3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphgxsr5_c/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphgxsr5_c/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_4jsg737/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_4jsg737/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9x1_twet/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9x1_twet/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0feovf4c/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0feovf4c/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmplqip15to/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplqip15to/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphu6o1mjz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphu6o1mjz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbd8i92ul/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbd8i92ul/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnytqv6cw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnytqv6cw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcf86fozn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcf86fozn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp297ktby6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp297ktby6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpkxukiohj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkxukiohj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmprukauqah/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprukauqah/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_qnsv_dr/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_qnsv_dr/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7wfoe4u9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7wfoe4u9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpht7n6ttx/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpht7n6ttx/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpuxee12wk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuxee12wk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpou0bqgys/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpou0bqgys/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpb5aglbyf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpb5aglbyf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpk4q2_54n/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk4q2_54n/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpq3dfs2ai/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpq3dfs2ai/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_x9iytji/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_x9iytji/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpleflrzq8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpleflrzq8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjxqp1b5f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjxqp1b5f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphs6gr0qy/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphs6gr0qy/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvh5j2ikk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvh5j2ikk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpyut15ccz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyut15ccz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp06wxdr96/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp06wxdr96/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1gxw_4zo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1gxw_4zo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmptsatokdv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptsatokdv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_v0mkc3d/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_v0mkc3d/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvtdkibmr/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvtdkibmr/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmph_2ctmng/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph_2ctmng/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpyjf64lbc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyjf64lbc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvtplk0rq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvtplk0rq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpyf6wgogm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyf6wgogm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpp8i2ulzv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp8i2ulzv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpv0w_frwc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpv0w_frwc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbdjshanv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbdjshanv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpo8uyd78g/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo8uyd78g/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgn2wt_fk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgn2wt_fk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1u0qo79t/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1u0qo79t/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7sdlxhr0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7sdlxhr0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp907po126/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp907po126/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp26owxpu0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp26owxpu0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0uexzhl8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0uexzhl8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpd6pf_7gv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd6pf_7gv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnngzsy23/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnngzsy23/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8nsy2zpr/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8nsy2zpr/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpv96ry6a3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpv96ry6a3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0qzycwdu/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0qzycwdu/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpj_uswkks/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpj_uswkks/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgo2aq0zk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgo2aq0zk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpa4s4hchu/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpa4s4hchu/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp73r313l2/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp73r313l2/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4hk2qs1m/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4hk2qs1m/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_3fbtj4_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_3fbtj4_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpv0t9n4p3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpv0t9n4p3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6wtcxld_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6wtcxld_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpk1flirzc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk1flirzc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvltv35it/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvltv35it/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4p1jkq_m/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4p1jkq_m/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp04qqe267/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp04qqe267/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7q289_f5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7q289_f5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2m3rlxt5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2m3rlxt5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp05wui4d3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp05wui4d3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1g68y8qq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1g68y8qq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpm3r9vhun/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm3r9vhun/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4c6xoc99/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4c6xoc99/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp56pozx7_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp56pozx7_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpj0uc9i75/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpj0uc9i75/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_7nerih4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_7nerih4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1lse6wpw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1lse6wpw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpu1zuw35t/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu1zuw35t/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp95xk6yjw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp95xk6yjw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphp6lju04/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphp6lju04/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpmjil1tn6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmjil1tn6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpkxbyj9q2/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkxbyj9q2/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpfkcx0yeb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfkcx0yeb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0le0amna/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0le0amna/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpy6qjm99n/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpy6qjm99n/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp82rvckuo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp82rvckuo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3hd2cvfl/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3hd2cvfl/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpph8q36bs/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpph8q36bs/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphtewiar0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphtewiar0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmph0ersy6_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph0ersy6_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7tfmzwro/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7tfmzwro/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwlkni7i_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwlkni7i_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdoe2a5er/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdoe2a5er/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpe585d160/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe585d160/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpadshzc_m/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpadshzc_m/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpw5ah_39w/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpw5ah_39w/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwqjt7l0f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwqjt7l0f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpmgxzaodv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmgxzaodv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7pa8eksc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7pa8eksc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqhogegw1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqhogegw1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpt95wacpk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpt95wacpk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpy2563wr_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpy2563wr_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp2im0m4xg/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2im0m4xg/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpklstxx6k/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpklstxx6k/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpfyw1ie85/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfyw1ie85/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpd5cgprfn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd5cgprfn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxd1xw7vw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxd1xw7vw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphdrnvda5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphdrnvda5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpp74xsm35/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp74xsm35/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpr68fk5n9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpr68fk5n9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp45pfigz2/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp45pfigz2/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpchi1bfi2/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpchi1bfi2/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpn8dsf63c/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpn8dsf63c/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0233ro0d/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0233ro0d/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpmr9xz1h7/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmr9xz1h7/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpf2usknzx/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf2usknzx/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9qwlmpwk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9qwlmpwk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpk_lk_bl8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk_lk_bl8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpi09cupb1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi09cupb1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp83wiain6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp83wiain6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4y1p6lic/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4y1p6lic/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4im_zk73/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4im_zk73/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbxh6hq1f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbxh6hq1f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpf2hub8ub/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf2hub8ub/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9jgzpjhg/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9jgzpjhg/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpg36ujhr1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpg36ujhr1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1byerc1_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1byerc1_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpuq6jo0i0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuq6jo0i0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp6phjvvpu/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6phjvvpu/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpuu27ehdb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuu27ehdb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpipms74xw/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpipms74xw/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpg5n1ry3l/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpg5n1ry3l/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpkhurjdmd/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkhurjdmd/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_bg4_716/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_bg4_716/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvycyl37y/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvycyl37y/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpuqm2zxq5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuqm2zxq5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpk6h8bmyc/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk6h8bmyc/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgfxnaw30/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgfxnaw30/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp0bi6om97/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0bi6om97/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpb3c20r6c/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpb3c20r6c/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzbf5wyv_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzbf5wyv_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpu37iyfqd/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu37iyfqd/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_zvjw_tq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_zvjw_tq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzc5zswhu/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzc5zswhu/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpsmskbl93/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsmskbl93/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpf8jd3t90/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf8jd3t90/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpl04w7io4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpl04w7io4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwt033d8f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwt033d8f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbd5c2wn7/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbd5c2wn7/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1djg8329/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1djg8329/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpwcollpfj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwcollpfj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjt3qjwl1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjt3qjwl1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpvfk0ybua/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvfk0ybua/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpgb0dz4t4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgb0dz4t4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpnskyamsp/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnskyamsp/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpth6aaz67/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpth6aaz67/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4b8g59ls/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4b8g59ls/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcnsmlnjx/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcnsmlnjx/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcyxd8rwm/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcyxd8rwm/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpylz8bvhd/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpylz8bvhd/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_gs65j7z/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_gs65j7z/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppnd_nejf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppnd_nejf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzcfugs1f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzcfugs1f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpipiv0acj/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpipiv0acj/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpqb1o16h9/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqb1o16h9/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp92fzsang/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp92fzsang/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpt9zxxzqa/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpt9zxxzqa/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpse5eo01s/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpse5eo01s/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpyj6k4rgp/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyj6k4rgp/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbkmo9mjt/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbkmo9mjt/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpuzf096uv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuzf096uv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpk2ktv_yo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk2ktv_yo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbyh8iqr_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbyh8iqr_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpkl0rpew3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkl0rpew3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp75p28izo/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp75p28izo/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpn9fakizz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpn9fakizz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3agw17t7/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3agw17t7/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcnfzlyt0/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcnfzlyt0/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphpif9frb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphpif9frb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp_es7xoog/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_es7xoog/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpo6ioild6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo6ioild6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpv71wt85b/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpv71wt85b/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp12ure49i/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp12ure49i/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpa2lbasna/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpa2lbasna/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppasptvv3/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppasptvv3/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp7puvk0zv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7puvk0zv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpyba9yeo4/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyba9yeo4/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpevhf3chl/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpevhf3chl/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdrr4kqcn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdrr4kqcn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpogl6xv_z/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpogl6xv_z/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpeyvt0_6i/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpeyvt0_6i/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp54izpy6k/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp54izpy6k/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzkjcarak/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzkjcarak/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpm5jptoxb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm5jptoxb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpk6jd_wdq/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk6jd_wdq/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpa1p65hv2/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpa1p65hv2/f2.bed | bedtools merge -c 4,5,6 -o first -i -) _______________________ test_nearest[upstream-True-same] _______________________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.Start, ocdf.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_ends.values - 1, right_starts.values, right_indexes) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 130 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGBEiTBARADi9Axg=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.End) | ^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 125 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQEQA4qQMW') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | ~~~~~~~~~~~~~~~~~~~^ | lcol, | ^^^^^ | ...<12 lines>... | check_flags=False, | ^^^^^^^^^^^^^^^^^^ | ) | ^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 471 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpey7e79sw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpey7e79sw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfmrl9qgc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfmrl9qgc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6alh1alh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6alh1alh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbsl23red/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbsl23red/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbmhtesli/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbmhtesli/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm56pqj4_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm56pqj4_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnlne416k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnlne416k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc7b1_z_q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc7b1_z_q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj8h_5q5s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj8h_5q5s/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 6203 + 0 1 chr1 69894 75791 - 0 2 chr1 5701693 5709454 + 0 3 chr1 6780898 6788586 + 0 4 chr1 7794839 7799727 - 0 5 chr1 8625626 8631677 - 0 6 chr19 7382337 7384521 - 0 7 chr21 7713255 7722909 - 0 8 chr22 2989792 2997915 - 0 9 chr3 2726960 2735554 + 0 10 chr7 7349942 7349943 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 6203 | a | 0 | ... | | chr1 | 6780898 | 6788586 | a | 0 | ... | | chr1 | 5701693 | 5709454 | a | 0 | ... | | chr1 | 69894 | 75791 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr7 | 7349942 | 7349943 | a | 0 | ... | | chr19 | 7382337 | 7384521 | a | 0 | ... | | chr21 | 7713255 | 7722909 | a | 0 | ... | | chr22 | 2989792 | 2997915 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 6203 + 0 3 chr1 69894 75791 - 0 6 chr3 2726960 2735554 + 0 10 chr22 2989792 2997915 - 0 2 chr1 5701693 5709454 + 0 1 chr1 6780898 6788586 + 0 7 chr7 7349942 7349943 + 0 8 chr19 7382337 7384521 - 0 9 chr21 7713255 7722909 - 0 4 chr1 7794839 7799727 - 0 5 chr1 8625626 8631677 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 6203 + 0 1 chr1 69894 75791 - 0 9 chr3 2726960 2735554 + 0 8 chr22 2989792 2997915 - 0 2 chr1 5701693 5709454 + 0 3 chr1 6780898 6788586 + 0 10 chr7 7349942 7349943 + 0 6 chr19 7382337 7384521 - 0 7 chr21 7713255 7722909 - 0 4 chr1 7794839 7799727 - 0 5 chr1 8625626 8631677 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 6203 + 0 1 chr1 69894 75791 - 0 2 chr1 5701693 5709454 + 0 3 chr1 6780898 6788586 + 0 4 chr1 7794839 7799727 - 0 5 chr1 8625626 8631677 - 0 6 chr19 7382337 7384521 - 0 7 chr21 7713255 7722909 - 0 8 chr22 2989792 2997915 - 0 9 chr3 2726960 2735554 + 0 10 chr7 7349942 7349943 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 6203 + 0 1 chr1 69894 75791 - 0 2 chr1 5701693 5709454 + 0 3 chr1 6780898 6788586 + 0 4 chr1 7794839 7799727 - 0 5 chr1 8625626 8631677 - 0 6 chr19 7382337 7384521 - 0 7 chr21 7713255 7722909 - 0 8 chr22 2989792 2997915 - 0 9 chr3 2726960 2735554 + 0 10 chr7 7349942 7349943 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps_hgufo3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps_hgufo3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd8atnvqj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd8atnvqj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfzw99zc0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfzw99zc0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz7ug29gy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz7ug29gy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplsbfxrlh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplsbfxrlh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgobjy5wf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgobjy5wf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyl3hq_0u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyl3hq_0u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsuk5leyj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsuk5leyj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpszjrp0e9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpszjrp0e9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps4qi7x2q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps4qi7x2q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpont6wkkv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpont6wkkv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt6yfetav/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt6yfetav/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_7u9f_p4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7u9f_p4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8hiqk08p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8hiqk08p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0002guud/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0002guud/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi3aqlz2x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi3aqlz2x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3yct_ehn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3yct_ehn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc84xxlrc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc84xxlrc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo9kkw4gm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo9kkw4gm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprlaezk47/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprlaezk47/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppetjc6b3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppetjc6b3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2vkwfjk9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2vkwfjk9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3dzxcyu3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3dzxcyu3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp23kt_ofb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp23kt_ofb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpubgwad53/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpubgwad53/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqutrxk8j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqutrxk8j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2x2wfije/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2x2wfije/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzjp8ryzk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzjp8ryzk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl0v7b6ts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0v7b6ts/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpekw2l1z7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpekw2l1z7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0iep9wtr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0iep9wtr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbt96vnov/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbt96vnov/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps76lc7nl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps76lc7nl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptxg30byw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptxg30byw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7enhv08u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7enhv08u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph4h7rgrq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph4h7rgrq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsau5vafj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsau5vafj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0vyj7g0u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0vyj7g0u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp47_n65ta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp47_n65ta/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa729bs6j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa729bs6j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt27wl_u0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt27wl_u0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptbtkfk10/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptbtkfk10/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdcka3c5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdcka3c5a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2qm9rig1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2qm9rig1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplwx29aem/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplwx29aem/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwn0gkobf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwn0gkobf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpihtl7j84/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpihtl7j84/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqfz2spch/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqfz2spch/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9k8mnzeu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9k8mnzeu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmposzxgp9f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmposzxgp9f/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6acz5c7t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6acz5c7t/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp54o47ubn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp54o47ubn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgs6kj_i9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgs6kj_i9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjh3rznpv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjh3rznpv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbuvzeztu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbuvzeztu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpry7nh2iy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpry7nh2iy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7_o72waq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7_o72waq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplbjqbmop/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplbjqbmop/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3v15eiwj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3v15eiwj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkvrse_h8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkvrse_h8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplngljwzg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplngljwzg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuvtev5pf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuvtev5pf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgqt15fan/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgqt15fan/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4xgrk9_m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4xgrk9_m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuajajb4h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuajajb4h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx0kjg5t8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx0kjg5t8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpes_ca38g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpes_ca38g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpenxivbnv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpenxivbnv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj21bbwul/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj21bbwul/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpalzjj2t4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpalzjj2t4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnj66w4s4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnj66w4s4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaghlh5r9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaghlh5r9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvqli2oxw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvqli2oxw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprim5a9qp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprim5a9qp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp87owtsvk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp87owtsvk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkzogajcw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkzogajcw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1lyci6l2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1lyci6l2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplx95f33p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplx95f33p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzxew1ovw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzxew1ovw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplk33tmyl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplk33tmyl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpctl0frc_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpctl0frc_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6zieug2y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6zieug2y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl44y2ma_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl44y2ma_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoztuuddr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoztuuddr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjytue00y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjytue00y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpacfaw_pb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpacfaw_pb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9rfrwnr1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9rfrwnr1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx8m57b7p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx8m57b7p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp53xoh0yk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp53xoh0yk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo6uko0aw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo6uko0aw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbfrygo6i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbfrygo6i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppe4vdpb7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppe4vdpb7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk1i740ec/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk1i740ec/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgkv875w1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgkv875w1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfia65jt1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfia65jt1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp930o39f4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp930o39f4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3sztmy_s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3sztmy_s/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjdgu21wp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjdgu21wp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8ctjyu53/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ctjyu53/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3j_62spg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3j_62spg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpru1xgqe2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpru1xgqe2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_7066gxg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7066gxg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc9bkbl3x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc9bkbl3x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvohxh8r3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvohxh8r3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu_zk_bk8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu_zk_bk8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz30h9ysz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz30h9ysz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3ilb6jji/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ilb6jji/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpubohp9cs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpubohp9cs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_g6f3q_8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_g6f3q_8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6lt2iirk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6lt2iirk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx1ql9_on/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx1ql9_on/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptrzg3k2z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptrzg3k2z/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsdjwkhd3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsdjwkhd3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8yuj3lc3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8yuj3lc3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2evqo3cp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2evqo3cp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjbqpjdad/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjbqpjdad/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgxl7geyo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgxl7geyo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzii0eiye/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzii0eiye/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxr4bme7s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxr4bme7s/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 4 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 4 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwci700iy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwci700iy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp557mw9ia/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp557mw9ia/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ni69i6j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ni69i6j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl5y9ydby/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl5y9ydby/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkl2ex4q9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkl2ex4q9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqnf_hyd0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqnf_hyd0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp25f90u5t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp25f90u5t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa9704mf7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa9704mf7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjtdy8ism/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjtdy8ism/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp58lb27jo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp58lb27jo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpem4qyz7e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpem4qyz7e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqmucqr0j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqmucqr0j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5j6r283v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5j6r283v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpahp_257b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpahp_257b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5d6k7rtr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5d6k7rtr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpohrf6uwg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpohrf6uwg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkkyz43yn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkkyz43yn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6hxlu1wt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6hxlu1wt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppgd8b7yg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppgd8b7yg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjeofhsdp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjeofhsdp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppqfavevt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppqfavevt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9lbkym4r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9lbkym4r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5tccs29d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5tccs29d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkrndp_3s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkrndp_3s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpibc_3nhr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpibc_3nhr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvgmunihz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvgmunihz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2v381105/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2v381105/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4uqnuwsg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4uqnuwsg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpydq895ra/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpydq895ra/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmwcoh19b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmwcoh19b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_xre5a9m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_xre5a9m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc5k67h0f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc5k67h0f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu_p3_wto/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu_p3_wto/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvm42_5wz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvm42_5wz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcyldbkd1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcyldbkd1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuyzjx1ap/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuyzjx1ap/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk2mlih29/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk2mlih29/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpor1jd6gb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpor1jd6gb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphrr7z3qt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphrr7z3qt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqflopq9y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqflopq9y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8vlacwc3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8vlacwc3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 4 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 4 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphtydd3r8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphtydd3r8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 4 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 4 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxvp6f8pf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxvp6f8pf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 4 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 4 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7_ikfpgx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7_ikfpgx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoqbd6r7d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoqbd6r7d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp1ia6n6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp1ia6n6y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy0_tded3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy0_tded3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd8152hu2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd8152hu2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 4 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 4 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj0_sfzjh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj0_sfzjh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ub2_ytm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ub2_ytm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaorddyx7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaorddyx7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprbllj18z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprbllj18z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbry5x7qt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbry5x7qt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkv171acn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkv171acn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmpbxmpan/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmpbxmpan/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbb0axpfh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbb0axpfh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv80ifbz3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv80ifbz3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyhclmvcy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyhclmvcy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjqxrjt73/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjqxrjt73/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxupjz5ne/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxupjz5ne/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1ucztlc5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ucztlc5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqkqqeq9q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqkqqeq9q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmcxt2_iy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmcxt2_iy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbb1xuoik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbb1xuoik/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi5bxt1e7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi5bxt1e7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0i_zqkwj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0i_zqkwj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpswfd5qd5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpswfd5qd5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxpjzxinz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxpjzxinz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8z9sqala/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8z9sqala/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 4 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 4 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp55c72rl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp55c72rl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppublpm6f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppublpm6f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzw31pvd_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzw31pvd_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyhdzo20x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyhdzo20x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdrauh0hk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdrauh0hk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkoc3uoz1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkoc3uoz1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe39pi05x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe39pi05x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7b_0ndhq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7b_0ndhq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmsvro_2f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmsvro_2f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwf0ptloz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwf0ptloz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl9wjx719/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl9wjx719/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4od5si7u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4od5si7u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgjreyafs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgjreyafs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqf26zr5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqf26zr5d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0xy64y_5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xy64y_5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnh0_dbai/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnh0_dbai/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqhphxnx7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqhphxnx7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmq8dji2b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmq8dji2b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvsb19bjv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvsb19bjv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpivaauias/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpivaauias/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp36dhxrxf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36dhxrxf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkr6aa_fs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkr6aa_fs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgpfd0mdh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgpfd0mdh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwdjeidr0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwdjeidr0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8d9lacyq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8d9lacyq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxdg3a64o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxdg3a64o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpghqn0wws/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpghqn0wws/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc1mho_lj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc1mho_lj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjpp6zv4k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjpp6zv4k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmv0e9yj5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmv0e9yj5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 5 + 0 1 chr1 1 5 + 0 2 chr1 1 5 + 0 3 chr1 1 5 + 0 4 chr1 1 5 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 5 | a | 0 | ... | | chr1 | 1 | 5 | a | 0 | ... | | chr1 | 1 | 5 | a | 0 | ... | | chr1 | 1 | 5 | a | 0 | ... | | chr1 | 1 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 5 + 0 1 chr1 1 5 + 0 2 chr1 1 5 + 0 3 chr1 1 5 + 0 4 chr1 1 5 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 5 + 0 1 chr1 1 5 + 0 2 chr1 1 5 + 0 3 chr1 1 5 + 0 4 chr1 1 5 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 5 + 0 1 chr1 1 5 + 0 2 chr1 1 5 + 0 3 chr1 1 5 + 0 4 chr1 1 5 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 5 + 0 1 chr1 1 5 + 0 2 chr1 1 5 + 0 3 chr1 1 5 + 0 4 chr1 1 5 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmruvw7a5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmruvw7a5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphyeoqn6p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphyeoqn6p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfgcmkovx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfgcmkovx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw6v5608u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw6v5608u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpasks7vto/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpasks7vto/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1b5ofo87/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1b5ofo87/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw43oft9m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw43oft9m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsqw8gt_v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsqw8gt_v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpalqa3dm2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpalqa3dm2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeqsymyq7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeqsymyq7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpomkqlkwx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpomkqlkwx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprao0oasq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprao0oasq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps3vmlytv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps3vmlytv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps9c205xp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps9c205xp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkxdf0wtu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkxdf0wtu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3q3glqaj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3q3glqaj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwrepkxlo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwrepkxlo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkp6b0w3b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkp6b0w3b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5g6tfamm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5g6tfamm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3_xua_9d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3_xua_9d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuuc2wn88/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuuc2wn88/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9mhpj4bo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9mhpj4bo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcl8m1ang/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcl8m1ang/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpov95cf6h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpov95cf6h/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfpsyjh9z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfpsyjh9z/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 4 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 4 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3oayyjqp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3oayyjqp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdnqv49p9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdnqv49p9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprd9zpxws/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprd9zpxws/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw1v9eu44/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw1v9eu44/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5zsnnnb3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5zsnnnb3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpft6xeyip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpft6xeyip/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9k4pvtbp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9k4pvtbp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpktdweot6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpktdweot6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpur0t1iyl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpur0t1iyl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg4np2ykt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg4np2ykt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa0_0p2sl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa0_0p2sl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbmhp3met/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbmhp3met/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 4 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 4 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps24626pr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps24626pr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp39jt_imt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp39jt_imt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbbykjilk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbbykjilk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwn9gd1z2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwn9gd1z2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqg0r080f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqg0r080f/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcy1skshp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcy1skshp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2igfuz0a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2igfuz0a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxx7nr09a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxx7nr09a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptml4gf2d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptml4gf2d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6qn1yn8o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6qn1yn8o/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi1hohgf8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi1hohgf8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprur73cww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprur73cww/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqpv5u__h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqpv5u__h/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1rv0q8uw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1rv0q8uw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1i7ckxzf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1i7ckxzf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9n3zzrsh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9n3zzrsh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp00drwnck/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00drwnck/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiw82n3ya/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiw82n3ya/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkrufoo_0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkrufoo_0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp250ydjda/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp250ydjda/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfeo646z_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfeo646z_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptae2d87n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptae2d87n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1x8_racv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1x8_racv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo0xwaa3x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo0xwaa3x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 5 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 5 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1zcv5yv8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1zcv5yv8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnaeo368x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnaeo368x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph154uxga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph154uxga/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4i7c5h0a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4i7c5h0a/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq3c43f0f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq3c43f0f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpny5w4ou1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpny5w4ou1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppr85ppai/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppr85ppai/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplzsx6h6k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplzsx6h6k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5up6fg_8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5up6fg_8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfnl8w_ag/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfnl8w_ag/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp004copya/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp004copya/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2skuz3rs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2skuz3rs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi1xrkbcd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi1xrkbcd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuwjhrfe2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuwjhrfe2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkbb7veuc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkbb7veuc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp98orup6v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp98orup6v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvcyssll5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvcyssll5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpom5m8vp1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpom5m8vp1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpakd8deoz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpakd8deoz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpng7s2y4t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpng7s2y4t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsnt0rtdh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsnt0rtdh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps2dwpfuf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps2dwpfuf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptf0m9g59/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptf0m9g59/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz65gc55n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz65gc55n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 5 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 5 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx0klyrkd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx0klyrkd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuop5p5vc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuop5p5vc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3zc8lr3p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3zc8lr3p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphcbu17ol/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphcbu17ol/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphtbf824g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphtbf824g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp91h0grun/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp91h0grun/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaannxrs5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaannxrs5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpevx_97kx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpevx_97kx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprjzkwf2r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprjzkwf2r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6lh1oi3s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6lh1oi3s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi_rntjyq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi_rntjyq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpslydtloe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpslydtloe/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq9w34u3y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9w34u3y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcdv91ph7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcdv91ph7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpauaydw9_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpauaydw9_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgssyy9bk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgssyy9bk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptj0clxb5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptj0clxb5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsy7vrsy7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsy7vrsy7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp34f3jn7g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp34f3jn7g/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm9x462r4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm9x462r4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb4a41soh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb4a41soh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7i0_wisd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7i0_wisd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc31cilae/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc31cilae/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuk5cckb3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuk5cckb3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps450qob9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps450qob9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpksm5rhdo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpksm5rhdo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph2tid692/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph2tid692/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeg51qc6o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeg51qc6o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpunn37j3c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpunn37j3c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwkthpry5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwkthpry5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxtjqpm4q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxtjqpm4q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpklo8dx1t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpklo8dx1t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb190tsyn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb190tsyn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqrsk_x8n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqrsk_x8n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbpvr976q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbpvr976q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp3c3w_6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp3c3w_6y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps2u41s41/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps2u41s41/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpytoybfnb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpytoybfnb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpme6b67ur/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpme6b67ur/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd9ytg0pa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd9ytg0pa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn_dzuxbv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn_dzuxbv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnits1prs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnits1prs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0h66_par/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0h66_par/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps63u8p7o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps63u8p7o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx1d5saxx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx1d5saxx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx3w77j_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3w77j_x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplo1n9ovv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplo1n9ovv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6fha_m2k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6fha_m2k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphsig51dk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphsig51dk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ___________ test_three_in_a_row[strandedness_chain47-method_chain47] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') _____________________________ test_coverage[same] ______________________________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", strandedness) tests/test_binary.py:207: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:238: in test_coverage result = gr.coverage(gr2, strandedness=strandedness) pyranges/pyranges.py:1341: in coverage other = other.merge(count=True, strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_coverage( E # The test always failed when commented parts were varied together. E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_8yg57p1/f1.bed -b /tmp/tmp_8yg57p1/f2.bed Chromosome Start End Name Score Strand 0 chr1 7438262 7438263 a 0 + 1 chr1 7346868 7354324 a 0 - 2 chr1 2394206 2400634 a 0 - 3 chr1 3397534 3397672 a 0 - 4 chr3 7823802 7833010 a 0 + 5 chr9 572552 576823 a 0 - 6 chr15 5195374 5198482 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9068 a 0 + 1 chr1 8472850 8480544 a 0 + 2 chr1 6135580 6137077 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpu92wfrs6/f1.bed -b /tmp/tmpu92wfrs6/f2.bed Chromosome Start End Name Score Strand 0 chr1 7438262 7438263 a 0 + 1 chr1 7346868 7354324 a 0 - 2 chr1 2394206 2400634 a 0 - 3 chr1 3397534 3397672 a 0 - 4 chr3 7823802 7833010 a 0 + 5 chr9 572552 576823 a 0 - 6 chr15 5195374 5198482 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9068 a 0 + 1 chr1 8472850 8480544 a 0 + 2 chr1 6135580 6137077 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpu5f_9_ux/f1.bed -b /tmp/tmpu5f_9_ux/f2.bed Chromosome Start End Name Score Strand 0 chr1 7438262 7438263 a 0 + 1 chr1 7346868 7354324 a 0 - 2 chr1 7456 13884 a 0 - 3 chr1 3397534 3397672 a 0 - 4 chr3 7823802 7833010 a 0 + 5 chr9 572552 576823 a 0 - 6 chr15 5195374 5198482 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9068 a 0 + 1 chr1 8472850 8480544 a 0 + 2 chr1 6135580 6137077 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpit1ol5tc/f1.bed -b /tmp/tmpit1ol5tc/f2.bed Chromosome Start End Name Score Strand 0 chr1 7438262 7438263 a 0 + 1 chr1 7346868 7354324 a 0 - 2 chr1 7456 13884 a 0 - 3 chr1 3397534 3397672 a 0 - 4 chr3 7823802 7833010 a 0 + 5 chr9 572552 576823 a 0 - 6 chr15 5195374 5198482 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpuizdbzqh/f1.bed -b /tmp/tmpuizdbzqh/f2.bed Chromosome Start End Name Score Strand 0 chr1 7438262 7438263 a 0 + 1 chr1 7346868 7354324 a 0 - 2 chr1 7456 13884 a 0 - 3 chr1 3397534 3397672 a 0 - 4 chr3 7823802 7833010 a 0 + 5 chr9 572552 576823 a 0 - 6 chr15 5195374 5198482 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpzbybr06i/f1.bed -b /tmp/tmpzbybr06i/f2.bed Chromosome Start End Name Score Strand 0 chr1 7438262 7438263 a 0 + 1 chr1 7346868 7354324 a 0 - 2 chr1 7456 13884 a 0 - 3 chr1 3397534 3397672 a 0 - 4 chr3 7823802 7833010 a 0 + 5 chr9 572552 576823 a 0 - 6 chr15 5195374 5198482 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + 5 chr1 1 2 a 0 + 6 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpa04l4kmz/f1.bed -b /tmp/tmpa04l4kmz/f2.bed Chromosome Start End Name Score Strand 0 chr1 7438262 7438263 a 0 + 1 chr1 7346868 7354324 a 0 - 2 chr1 7456 13884 a 0 - 3 chr1 3397534 3397672 a 0 - 4 chr3 7823802 7833010 a 0 + 5 chr9 572552 576823 a 0 - 6 chr15 5195374 5198482 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + 5 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpr1bxb8qx/f1.bed -b /tmp/tmpr1bxb8qx/f2.bed Chromosome Start End Name Score Strand 0 chr1 4236193 4239735 a 0 - 1 chr11 1920428 1923255 a 0 + Chromosome Start End Name Score Strand 0 chr1 2505288 2511248 a 0 + 1 chr1 8229657 8229820 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3wfvfzm2/f1.bed -b /tmp/tmp3wfvfzm2/f2.bed Chromosome Start End Name Score Strand 0 chr1 4236193 4239735 a 0 - 1 chr11 1920428 1923255 a 0 + Chromosome Start End Name Score Strand 0 chr1 2505288 2511248 a 0 + 1 chr1 3498536 3498699 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0gey2tsy/f1.bed -b /tmp/tmp0gey2tsy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3z3j0ctw/f1.bed -b /tmp/tmp3z3j0ctw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpmrh30amo/f1.bed -b /tmp/tmpmrh30amo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpo_l26o19/f1.bed -b /tmp/tmpo_l26o19/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxpanaapb/f1.bed -b /tmp/tmpxpanaapb/f2.bed Chromosome Start End Name Score Strand 0 chr1 7404 7405 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9291 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp62l8f2b6/f1.bed -b /tmp/tmp62l8f2b6/f2.bed Chromosome Start End Name Score Strand 0 chr1 7404 7405 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpj4wy2br4/f1.bed -b /tmp/tmpj4wy2br4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr14 6832008 6832177 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp59isd7om/f1.bed -b /tmp/tmp59isd7om/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpg84uqaj2/f1.bed -b /tmp/tmpg84uqaj2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2763119 2770274 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpmzjs69t3/f1.bed -b /tmp/tmpmzjs69t3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpa578by3n/f1.bed -b /tmp/tmpa578by3n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9186087 9190352 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp94_xu0b4/f1.bed -b /tmp/tmp94_xu0b4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmplmsw8ioc/f1.bed -b /tmp/tmplmsw8ioc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4025813 4034670 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpcmw5ky9d/f1.bed -b /tmp/tmpcmw5ky9d/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpd7_ca5wq/f1.bed -b /tmp/tmpd7_ca5wq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8446321 8454493 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpn9jab4b1/f1.bed -b /tmp/tmpn9jab4b1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdfolh55m/f1.bed -b /tmp/tmpdfolh55m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4939521 4943606 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9955flr5/f1.bed -b /tmp/tmp9955flr5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpx4j2blwl/f1.bed -b /tmp/tmpx4j2blwl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3108492 3117594 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwaoulmgf/f1.bed -b /tmp/tmpwaoulmgf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpgucrgqfa/f1.bed -b /tmp/tmpgucrgqfa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 1173 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpzchqiy7f/f1.bed -b /tmp/tmpzchqiy7f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpptel8xt4/f1.bed -b /tmp/tmpptel8xt4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4689326 4691216 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdw05dzm3/f1.bed -b /tmp/tmpdw05dzm3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2cm09v80/f1.bed -b /tmp/tmp2cm09v80/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6397806 6406962 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmptuhss3os/f1.bed -b /tmp/tmptuhss3os/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpodr2wac2/f1.bed -b /tmp/tmpodr2wac2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6048923 6053624 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpo9kuboez/f1.bed -b /tmp/tmpo9kuboez/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphg3eem3e/f1.bed -b /tmp/tmphg3eem3e/f2.bed Chromosome Start End Name Score Strand 0 chr1 2327 2328 a 0 - 1 chr1 2327 2328 a 0 - Chromosome Start End Name Score Strand 0 chr1 10000000 10009977 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp69b29dfh/f1.bed -b /tmp/tmp69b29dfh/f2.bed Chromosome Start End Name Score Strand 0 chr1 2327 2328 a 0 - 1 chr1 2327 2328 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpcir13q1z/f1.bed -b /tmp/tmpcir13q1z/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr8 3757845 3759179 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpco2qkr2c/f1.bed -b /tmp/tmpco2qkr2c/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpgcsd0k_7/f1.bed -b /tmp/tmpgcsd0k_7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 937932 945999 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmppav3uafw/f1.bed -b /tmp/tmppav3uafw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvoogahby/f1.bed -b /tmp/tmpvoogahby/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr6 1416726 1424447 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9tjgdd9q/f1.bed -b /tmp/tmp9tjgdd9q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp91_lf08o/f1.bed -b /tmp/tmp91_lf08o/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4485724 4488360 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpudly3g50/f1.bed -b /tmp/tmpudly3g50/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp64qf78e5/f1.bed -b /tmp/tmp64qf78e5/f2.bed Chromosome Start End Name Score Strand 0 chr1 5115 5116 a 0 - 1 chr1 5115 5116 a 0 - Chromosome Start End Name Score Strand 0 chr1 1098127 1108072 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp41ia4m7z/f1.bed -b /tmp/tmp41ia4m7z/f2.bed Chromosome Start End Name Score Strand 0 chr1 5115 5116 a 0 - 1 chr1 5115 5116 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqkgqyqld/f1.bed -b /tmp/tmpqkgqyqld/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8764495 8765600 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpnb3sqhfi/f1.bed -b /tmp/tmpnb3sqhfi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpoud7au_g/f1.bed -b /tmp/tmpoud7au_g/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr7 8366557 8375363 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphfibrtiz/f1.bed -b /tmp/tmphfibrtiz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp63tcm4mw/f1.bed -b /tmp/tmp63tcm4mw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8748336 8753200 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmppc2nbwbe/f1.bed -b /tmp/tmppc2nbwbe/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpruydiuj7/f1.bed -b /tmp/tmpruydiuj7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1431762 1436170 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjaign9ii/f1.bed -b /tmp/tmpjaign9ii/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpr9r7pxu8/f1.bed -b /tmp/tmpr9r7pxu8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9999999 10000413 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpche3gzor/f1.bed -b /tmp/tmpche3gzor/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphff1ubod/f1.bed -b /tmp/tmphff1ubod/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7946539 7949800 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpp1os05gg/f1.bed -b /tmp/tmpp1os05gg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmptosfgs05/f1.bed -b /tmp/tmptosfgs05/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8609767 8613607 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpuagbeuk6/f1.bed -b /tmp/tmpuagbeuk6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmppckis76p/f1.bed -b /tmp/tmppckis76p/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7460924 7466909 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9e8faudk/f1.bed -b /tmp/tmp9e8faudk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpcrzjnu1i/f1.bed -b /tmp/tmpcrzjnu1i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7063540 7065234 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpy881tmfv/f1.bed -b /tmp/tmpy881tmfv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpx0ifzwtj/f1.bed -b /tmp/tmpx0ifzwtj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7476071 7481547 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpc068d9cp/f1.bed -b /tmp/tmpc068d9cp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp1hjwqxah/f1.bed -b /tmp/tmp1hjwqxah/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 4732 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp37f2ed1q/f1.bed -b /tmp/tmp37f2ed1q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmprh3g3j6m/f1.bed -b /tmp/tmprh3g3j6m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1668083 1676645 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0xne1w5y/f1.bed -b /tmp/tmp0xne1w5y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpx1re2pbf/f1.bed -b /tmp/tmpx1re2pbf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2125972 2130521 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpm06ae9l1/f1.bed -b /tmp/tmpm06ae9l1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpuon56yjj/f1.bed -b /tmp/tmpuon56yjj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4883577 4888349 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpb8gjw1wz/f1.bed -b /tmp/tmpb8gjw1wz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdoi1bqf6/f1.bed -b /tmp/tmpdoi1bqf6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6989723 6999722 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp6q76q169/f1.bed -b /tmp/tmp6q76q169/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp62qfe5xt/f1.bed -b /tmp/tmp62qfe5xt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 305322 306752 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2dipu3fx/f1.bed -b /tmp/tmp2dipu3fx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp6l6lbsht/f1.bed -b /tmp/tmp6l6lbsht/f2.bed Chromosome Start End Name Score Strand 0 chr1 307 308 a 0 - 1 chr1 307 308 a 0 - Chromosome Start End Name Score Strand 0 chr1 7883457 7892700 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpk2igq8p5/f1.bed -b /tmp/tmpk2igq8p5/f2.bed Chromosome Start End Name Score Strand 0 chr1 307 308 a 0 - 1 chr1 307 308 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdx1cebhq/f1.bed -b /tmp/tmpdx1cebhq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9999999 10003086 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpisganzcr/f1.bed -b /tmp/tmpisganzcr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsqvx4m2u/f1.bed -b /tmp/tmpsqvx4m2u/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr14 6084400 6090632 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpmiq077bb/f1.bed -b /tmp/tmpmiq077bb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpv0wmg6m2/f1.bed -b /tmp/tmpv0wmg6m2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3310784 3316920 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphjb6nxwk/f1.bed -b /tmp/tmphjb6nxwk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp09em8s4b/f1.bed -b /tmp/tmp09em8s4b/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6031872 6036758 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpzggnndfw/f1.bed -b /tmp/tmpzggnndfw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjecmqth2/f1.bed -b /tmp/tmpjecmqth2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chrX 3140577 3150556 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpk5cbjmvn/f1.bed -b /tmp/tmpk5cbjmvn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmplu46wo2v/f1.bed -b /tmp/tmplu46wo2v/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6050602 6060345 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp02zchy2s/f1.bed -b /tmp/tmp02zchy2s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpb_d5p36s/f1.bed -b /tmp/tmpb_d5p36s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4369594 4372491 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpplvus585/f1.bed -b /tmp/tmpplvus585/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpgseg85nr/f1.bed -b /tmp/tmpgseg85nr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6277878 6286227 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvy1rg4_t/f1.bed -b /tmp/tmpvy1rg4_t/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2gwcvusc/f1.bed -b /tmp/tmp2gwcvusc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5391796 5391974 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp68z4w22h/f1.bed -b /tmp/tmp68z4w22h/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpl0u46suf/f1.bed -b /tmp/tmpl0u46suf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3234686 3235920 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2q3bqzb_/f1.bed -b /tmp/tmp2q3bqzb_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwb424qj_/f1.bed -b /tmp/tmpwb424qj_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr14 302438 303193 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp7x8uxcq_/f1.bed -b /tmp/tmp7x8uxcq_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqhdh6rfw/f1.bed -b /tmp/tmpqhdh6rfw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 268242 276791 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp1ue27b8d/f1.bed -b /tmp/tmp1ue27b8d/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpy9uh7_v1/f1.bed -b /tmp/tmpy9uh7_v1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4391733 4396647 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmplha3ig8b/f1.bed -b /tmp/tmplha3ig8b/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphegxb7jc/f1.bed -b /tmp/tmphegxb7jc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 610714 612498 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3rmahya3/f1.bed -b /tmp/tmp3rmahya3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpv98_hp3k/f1.bed -b /tmp/tmpv98_hp3k/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2629710 2632989 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpka63xr2s/f1.bed -b /tmp/tmpka63xr2s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxtnw_7qf/f1.bed -b /tmp/tmpxtnw_7qf/f2.bed Chromosome Start End Name Score Strand 0 chr1 6885 6886 a 0 - 1 chr1 6885 6886 a 0 - Chromosome Start End Name Score Strand 0 chr1 936612 940876 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpu6n8shqt/f1.bed -b /tmp/tmpu6n8shqt/f2.bed Chromosome Start End Name Score Strand 0 chr1 6885 6886 a 0 - 1 chr1 6885 6886 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp83kjlzrc/f1.bed -b /tmp/tmp83kjlzrc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3887513 3888486 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmppvf0rhtv/f1.bed -b /tmp/tmppvf0rhtv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpt8pc_cha/f1.bed -b /tmp/tmpt8pc_cha/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 37741 42936 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxczi7n6h/f1.bed -b /tmp/tmpxczi7n6h/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp8bl7fess/f1.bed -b /tmp/tmp8bl7fess/f2.bed Chromosome Start End Name Score Strand 0 chr1 3980 3981 a 0 - 1 chr1 3980 3981 a 0 - Chromosome Start End Name Score Strand 0 chr1 9531098 9540335 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0u1q0rqi/f1.bed -b /tmp/tmp0u1q0rqi/f2.bed Chromosome Start End Name Score Strand 0 chr1 3980 3981 a 0 - 1 chr1 3980 3981 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp31pqlwez/f1.bed -b /tmp/tmp31pqlwez/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1162312 1164057 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpht1lkfvf/f1.bed -b /tmp/tmpht1lkfvf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpm3ntz9ah/f1.bed -b /tmp/tmpm3ntz9ah/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 940973 950219 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpe0apug1q/f1.bed -b /tmp/tmpe0apug1q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpb1lvnmzc/f1.bed -b /tmp/tmpb1lvnmzc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5308693 5313897 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphjh64uhz/f1.bed -b /tmp/tmphjh64uhz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp7p2xmy3_/f1.bed -b /tmp/tmp7p2xmy3_/f2.bed Chromosome Start End Name Score Strand 0 chr1 7216 7217 a 0 - 1 chr1 7216 7217 a 0 - Chromosome Start End Name Score Strand 0 chr1 3167490 3177248 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqcz58gnb/f1.bed -b /tmp/tmpqcz58gnb/f2.bed Chromosome Start End Name Score Strand 0 chr1 7216 7217 a 0 - 1 chr1 7216 7217 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2ymmsd1j/f1.bed -b /tmp/tmp2ymmsd1j/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2421319 2430284 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpo9ukn3o5/f1.bed -b /tmp/tmpo9ukn3o5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp44eeg4vz/f1.bed -b /tmp/tmp44eeg4vz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7413882 7421970 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpg__2v0gk/f1.bed -b /tmp/tmpg__2v0gk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4g_mgqrl/f1.bed -b /tmp/tmp4g_mgqrl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5076662 5079051 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmps6nl8kwf/f1.bed -b /tmp/tmps6nl8kwf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpneo6eloo/f1.bed -b /tmp/tmpneo6eloo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chrY 6046228 6047974 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_gryuqiz/f1.bed -b /tmp/tmp_gryuqiz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpue0a3bjs/f1.bed -b /tmp/tmpue0a3bjs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr11 202262 211356 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpep_5bvp5/f1.bed -b /tmp/tmpep_5bvp5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpbfifdo6b/f1.bed -b /tmp/tmpbfifdo6b/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4478920 4485304 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpey121fbc/f1.bed -b /tmp/tmpey121fbc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpcrgixs93/f1.bed -b /tmp/tmpcrgixs93/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2504260 2508406 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpcjnxxqjh/f1.bed -b /tmp/tmpcjnxxqjh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4q53qwij/f1.bed -b /tmp/tmp4q53qwij/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2069406 2073996 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp369d9oh8/f1.bed -b /tmp/tmp369d9oh8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9aq8d7sr/f1.bed -b /tmp/tmp9aq8d7sr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4842815 4851453 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxjthbsh2/f1.bed -b /tmp/tmpxjthbsh2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpnbcbre16/f1.bed -b /tmp/tmpnbcbre16/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr12 9411875 9412619 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpv_svy6zg/f1.bed -b /tmp/tmpv_svy6zg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9sk2d4fe/f1.bed -b /tmp/tmp9sk2d4fe/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6513767 6520273 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpfu46cllv/f1.bed -b /tmp/tmpfu46cllv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9li52po8/f1.bed -b /tmp/tmp9li52po8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxlne_4vy/f1.bed -b /tmp/tmpxlne_4vy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9795566 9803715 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0w7nh4zb/f1.bed -b /tmp/tmp0w7nh4zb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp7qa71bic/f1.bed -b /tmp/tmp7qa71bic/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9234752 9243554 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpja5bahg3/f1.bed -b /tmp/tmpja5bahg3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp6370uxlg/f1.bed -b /tmp/tmp6370uxlg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5544435 5548627 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmps402xugd/f1.bed -b /tmp/tmps402xugd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp8fvrhj7o/f1.bed -b /tmp/tmp8fvrhj7o/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr17 1431491 1441491 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsk1a8vmt/f1.bed -b /tmp/tmpsk1a8vmt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpg3iw7bxs/f1.bed -b /tmp/tmpg3iw7bxs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9665160 9671979 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpfhkghrsh/f1.bed -b /tmp/tmpfhkghrsh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpc2ib5t3w/f1.bed -b /tmp/tmpc2ib5t3w/f2.bed Chromosome Start End Name Score Strand 0 chr1 569 570 a 0 - 1 chr1 569 570 a 0 - Chromosome Start End Name Score Strand 0 chr1 1504113 1509129 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp14p7bfbn/f1.bed -b /tmp/tmp14p7bfbn/f2.bed Chromosome Start End Name Score Strand 0 chr1 569 570 a 0 - 1 chr1 569 570 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2f7g629q/f1.bed -b /tmp/tmp2f7g629q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr10 6511760 6520469 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmppnaq2azr/f1.bed -b /tmp/tmppnaq2azr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp1m4ggp49/f1.bed -b /tmp/tmp1m4ggp49/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9955301 9956299 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjbr8ovfc/f1.bed -b /tmp/tmpjbr8ovfc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmplpm043dz/f1.bed -b /tmp/tmplpm043dz/f2.bed Chromosome Start End Name Score Strand 0 chr13 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 7231 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp14ywhnt2/f1.bed -b /tmp/tmp14ywhnt2/f2.bed Chromosome Start End Name Score Strand 0 chr13 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpr6rqx7xk/f1.bed -b /tmp/tmpr6rqx7xk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 10000000 10009296 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpr_397d7f/f1.bed -b /tmp/tmpr_397d7f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpl2465hwz/f1.bed -b /tmp/tmpl2465hwz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2675584 2677870 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwjn33a98/f1.bed -b /tmp/tmpwjn33a98/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpd0t35s6n/f1.bed -b /tmp/tmpd0t35s6n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7158152 7165454 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpeu8ni2p0/f1.bed -b /tmp/tmpeu8ni2p0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjlj444dm/f1.bed -b /tmp/tmpjlj444dm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8391790 8393044 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpq3zso04e/f1.bed -b /tmp/tmpq3zso04e/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpotixmpus/f1.bed -b /tmp/tmpotixmpus/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9664127 9673010 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwelh31ps/f1.bed -b /tmp/tmpwelh31ps/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpshsp96m0/f1.bed -b /tmp/tmpshsp96m0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9585141 9589692 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpeqcozcw1/f1.bed -b /tmp/tmpeqcozcw1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpy5l9itmy/f1.bed -b /tmp/tmpy5l9itmy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7251618 7260779 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpywbrje51/f1.bed -b /tmp/tmpywbrje51/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmprb50n3qn/f1.bed -b /tmp/tmprb50n3qn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1378977 1385013 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp5_om7qz2/f1.bed -b /tmp/tmp5_om7qz2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_6riqx1c/f1.bed -b /tmp/tmp_6riqx1c/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1935149 1936912 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqhim5l_o/f1.bed -b /tmp/tmpqhim5l_o/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdf15ghh1/f1.bed -b /tmp/tmpdf15ghh1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 500956 505115 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpn8_7bbxb/f1.bed -b /tmp/tmpn8_7bbxb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp5jf71kns/f1.bed -b /tmp/tmp5jf71kns/f2.bed Chromosome Start End Name Score Strand 0 chr1 5321 5322 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 168 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpo2wx_g1h/f1.bed -b /tmp/tmpo2wx_g1h/f2.bed Chromosome Start End Name Score Strand 0 chr1 5321 5322 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjv7xm0_s/f1.bed -b /tmp/tmpjv7xm0_s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5105298 5105439 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmptu6cbhud/f1.bed -b /tmp/tmptu6cbhud/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3q68mp0g/f1.bed -b /tmp/tmp3q68mp0g/f2.bed Chromosome Start End Name Score Strand 0 chr1 2032 2033 a 0 - 1 chr1 2032 2033 a 0 - Chromosome Start End Name Score Strand 0 chr1 2079260 2079262 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp5g6gfi9l/f1.bed -b /tmp/tmp5g6gfi9l/f2.bed Chromosome Start End Name Score Strand 0 chr1 2032 2033 a 0 - 1 chr1 2032 2033 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_sd94_fq/f1.bed -b /tmp/tmp_sd94_fq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9999999 10005090 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpb_5zqh7q/f1.bed -b /tmp/tmpb_5zqh7q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp82defloh/f1.bed -b /tmp/tmp82defloh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4702215 4710424 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpe9epbely/f1.bed -b /tmp/tmpe9epbely/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvbce4u2w/f1.bed -b /tmp/tmpvbce4u2w/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2010496 2013432 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpuv6tuio0/f1.bed -b /tmp/tmpuv6tuio0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp82r066ii/f1.bed -b /tmp/tmp82r066ii/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3915402 3923704 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpfc15n0ff/f1.bed -b /tmp/tmpfc15n0ff/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpzxqz64zp/f1.bed -b /tmp/tmpzxqz64zp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr18 10000000 10003778 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp01kgb0k7/f1.bed -b /tmp/tmp01kgb0k7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2duk2p16/f1.bed -b /tmp/tmp2duk2p16/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5351047 5353218 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmptuhd_p9t/f1.bed -b /tmp/tmptuhd_p9t/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpi9fx_nz6/f1.bed -b /tmp/tmpi9fx_nz6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3957870 3958500 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvf1h_46w/f1.bed -b /tmp/tmpvf1h_46w/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphhifjek4/f1.bed -b /tmp/tmphhifjek4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 800646 809694 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpulhezwjw/f1.bed -b /tmp/tmpulhezwjw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpbdn9v6al/f1.bed -b /tmp/tmpbdn9v6al/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 5426 a 0 + 1 chr1 1 5426 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpon_1ezvv/f1.bed -b /tmp/tmpon_1ezvv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpfxq_0ml6/f1.bed -b /tmp/tmpfxq_0ml6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3006660 3014542 a 0 - 1 chr2 3543829 3550101 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp1cltmwuf/f1.bed -b /tmp/tmp1cltmwuf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1095658 1101750 a 0 + 1 chr1 1505992 1512353 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkvywfchz/f1.bed -b /tmp/tmpkvywfchz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 8555 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpnjhthhre/f1.bed -b /tmp/tmpnjhthhre/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8376357 8385001 a 0 - 1 chr20 5538494 5544628 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_qwq4qjt/f1.bed -b /tmp/tmp_qwq4qjt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9999163 10004713 a 0 + 1 chr1 9926834 9929837 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpx2mhkfy6/f1.bed -b /tmp/tmpx2mhkfy6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9337 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpy4gf1kzv/f1.bed -b /tmp/tmpy4gf1kzv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2725454 2734261 a 0 - 1 chr20 8763543 8765793 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp8vjb9yf4/f1.bed -b /tmp/tmp8vjb9yf4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1621443 1623843 a 0 + 1 chr1 324012 324057 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvupj73lx/f1.bed -b /tmp/tmpvupj73lx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 1619 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwnl5pwg2/f1.bed -b /tmp/tmpwnl5pwg2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5202448 5211899 a 0 - 1 chr1 5202448 5206743 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpn6xbek1m/f1.bed -b /tmp/tmpn6xbek1m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 3203 a 0 + 1 chr1 1 3203 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpe3z9vytr/f1.bed -b /tmp/tmpe3z9vytr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 1766 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwsuovw8i/f1.bed -b /tmp/tmpwsuovw8i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 6895 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpyhf4dnvt/f1.bed -b /tmp/tmpyhf4dnvt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7302688 7310597 a 0 + 1 chr1 9806145 9807940 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpj9op_78w/f1.bed -b /tmp/tmpj9op_78w/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 5643 a 0 + 1 chr1 1 5643 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9zy4_en3/f1.bed -b /tmp/tmp9zy4_en3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5646340 5648597 a 0 + 1 chr1 5646340 5654367 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpx6b_eso7/f1.bed -b /tmp/tmpx6b_eso7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9532580 9537294 a 0 + 1 chr1 6609099 6618659 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpn7_gfvb3/f1.bed -b /tmp/tmpn7_gfvb3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9470551 9480551 a 0 - 1 chr8 2081675 2081676 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp6qy3fs3c/f1.bed -b /tmp/tmp6qy3fs3c/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 7646 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3cfgdxcf/f1.bed -b /tmp/tmp3cfgdxcf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3693530 3698911 a 0 + 1 chr1 9822421 9822972 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpr20jxs_g/f1.bed -b /tmp/tmpr20jxs_g/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 63987 69652 a 0 - 1 chr1 9017513 9019714 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqkychgo9/f1.bed -b /tmp/tmpqkychgo9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2236425 2244451 a 0 + 1 chr1 2 7811 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpbi8ussu3/f1.bed -b /tmp/tmpbi8ussu3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2174617 2179248 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphwokxf3x/f1.bed -b /tmp/tmphwokxf3x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 707706 716630 a 0 - 1 chr15 2479948 2486767 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3hx_rrmd/f1.bed -b /tmp/tmp3hx_rrmd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3118612 3120354 a 0 + 1 chr1 226071 226073 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpa4n11e5y/f1.bed -b /tmp/tmpa4n11e5y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 5226 a 0 - 1 chr1 1 5226 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmptkztq9r9/f1.bed -b /tmp/tmptkztq9r9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3935951 3942709 a 0 + 1 chr1 6396945 6406275 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvbw274ju/f1.bed -b /tmp/tmpvbw274ju/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7033220 7041111 a 0 + 1 chr1 8284506 8292327 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpi4okn9b6/f1.bed -b /tmp/tmpi4okn9b6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2561070 2566062 a 0 + 1 chr1 4222690 4229384 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpq5hy3azn/f1.bed -b /tmp/tmpq5hy3azn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6365933 6375808 a 0 + 1 chr20 9178600 9184038 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpt62glan1/f1.bed -b /tmp/tmpt62glan1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6958980 6959484 a 0 + 1 chr1 4656831 4662173 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpn7oqb7cz/f1.bed -b /tmp/tmpn7oqb7cz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6530593 6532472 a 0 - 1 chr11 3128170 3137746 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpr7ljcjlp/f1.bed -b /tmp/tmpr7ljcjlp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1362000 1365380 a 0 + 1 chr1 10000000 10008118 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp7g3y7rzu/f1.bed -b /tmp/tmp7g3y7rzu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8961837 8964857 a 0 + 1 chr21 2678963 2682270 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4gwva4ak/f1.bed -b /tmp/tmp4gwva4ak/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8556504 8564041 a 0 - 1 chr1 2 2695 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpn6cda4xq/f1.bed -b /tmp/tmpn6cda4xq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 8193 a 0 - 1 chr1 1 8193 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp5dob60fs/f1.bed -b /tmp/tmp5dob60fs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4775753 4778645 a 0 + 1 chr1 3661986 3668474 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_nrh8odv/f1.bed -b /tmp/tmp_nrh8odv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6136407 6141358 a 0 - 1 chr16 3932160 3940792 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpuqdekw0m/f1.bed -b /tmp/tmpuqdekw0m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2909437 2918999 a 0 - 1 chr10 2740846 2746147 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp8sztw9uu/f1.bed -b /tmp/tmp8sztw9uu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 384754 391376 a 0 + 1 chr1 2708870 2717162 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpw20_xody/f1.bed -b /tmp/tmpw20_xody/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp5auxfq8q/f1.bed -b /tmp/tmp5auxfq8q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 647853 655510 a 0 + 1 chr1 4940147 4949497 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmprheimlwc/f1.bed -b /tmp/tmprheimlwc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1241241 1246246 a 0 + 1 chr1 3403125 3405374 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmppck_bw2e/f1.bed -b /tmp/tmppck_bw2e/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 7247 a 0 + 1 chr1 1 7247 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpcq6_yrle/f1.bed -b /tmp/tmpcq6_yrle/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1509911 1514620 a 0 - 1 chr1 7258862 7265602 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkux04ky_/f1.bed -b /tmp/tmpkux04ky_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9826314 9833932 a 0 + 1 chr1 5818310 5824839 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpx3s8obfk/f1.bed -b /tmp/tmpx3s8obfk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 1758 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2riy_u4r/f1.bed -b /tmp/tmp2riy_u4r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4627406 4633713 a 0 - 1 chr1 9766914 9772319 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpql4bxzzi/f1.bed -b /tmp/tmpql4bxzzi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9859847 9867358 a 0 + 1 chr13 8502689 8512688 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpfi62r86f/f1.bed -b /tmp/tmpfi62r86f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 7569 a 0 + 1 chr1 1 7569 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkmf32t2c/f1.bed -b /tmp/tmpkmf32t2c/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 842 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqogt8qcq/f1.bed -b /tmp/tmpqogt8qcq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9590 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpp9ybu4dl/f1.bed -b /tmp/tmpp9ybu4dl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9718579 9723050 a 0 - 1 chr18 2111180 2113014 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpf4pn4xj7/f1.bed -b /tmp/tmpf4pn4xj7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7825316 7835264 a 0 - 1 chrX 2112798 2116618 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp7najansv/f1.bed -b /tmp/tmp7najansv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4317326 4323615 a 0 + 1 chr1 4317326 4317555 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpemenyurp/f1.bed -b /tmp/tmpemenyurp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1780559 1784403 a 0 + 1 chr1 8707623 8714649 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp09v01c_d/f1.bed -b /tmp/tmp09v01c_d/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7642402 7643412 a 0 + 1 chr1 4053363 4053364 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp6fflru3o/f1.bed -b /tmp/tmp6fflru3o/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9189260 9197521 a 0 + 1 chr3 9362207 9362925 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpa9weyp66/f1.bed -b /tmp/tmpa9weyp66/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5059809 5064224 a 0 - 1 chr13 10000000 10009403 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp5zfk3sa6/f1.bed -b /tmp/tmp5zfk3sa6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 631196 632719 a 0 - 1 chr8 631196 635292 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpep3uwppa/f1.bed -b /tmp/tmpep3uwppa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2052442 2056925 a 0 + 1 chr5 1 6762 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp58xcymo0/f1.bed -b /tmp/tmp58xcymo0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6083007 6084297 a 0 + 1 chr1 433328 434618 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpume88bwt/f1.bed -b /tmp/tmpume88bwt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 5206 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpfewoox2f/f1.bed -b /tmp/tmpfewoox2f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9347 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp5ut5ve0a/f1.bed -b /tmp/tmp5ut5ve0a/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9069 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvq1cw_2i/f1.bed -b /tmp/tmpvq1cw_2i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1365139 1367888 a 0 + 1 chr1 1365139 1369830 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpnf2prymy/f1.bed -b /tmp/tmpnf2prymy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 3473 a 0 - 1 chr1 3177321 3182134 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphj4z076u/f1.bed -b /tmp/tmphj4z076u/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9901168 9903249 a 0 + 1 chr1 3949680 3952206 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpuov2xg4s/f1.bed -b /tmp/tmpuov2xg4s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 8899 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdis0zzok/f1.bed -b /tmp/tmpdis0zzok/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6466510 6468837 a 0 + 1 chr8 8105639 8105640 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_mbs4cs6/f1.bed -b /tmp/tmp_mbs4cs6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 10001 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpzd049g0t/f1.bed -b /tmp/tmpzd049g0t/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4505494 4511395 a 0 + 1 chr2 3454041 3459747 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpntpibj_7/f1.bed -b /tmp/tmpntpibj_7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 1986 a 0 + 1 chr1 1 1986 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmputewl4lc/f1.bed -b /tmp/tmputewl4lc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3924613 3924754 a 0 + 1 chr18 9548795 9549281 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpb8ozxwck/f1.bed -b /tmp/tmpb8ozxwck/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4411457 4414838 a 0 - 1 chrM 3662249 3672055 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpq_nglgzs/f1.bed -b /tmp/tmpq_nglgzs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 8962 a 0 - 1 chr1 1 8962 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpu9y7ec_5/f1.bed -b /tmp/tmpu9y7ec_5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2687574 2689206 a 0 - 1 chr8 1341325 1350804 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpq2uc5540/f1.bed -b /tmp/tmpq2uc5540/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9594729 9601618 a 0 - 1 chr11 787164 790554 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpz1vio_m0/f1.bed -b /tmp/tmpz1vio_m0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9948 a 0 + 1 chr18 7044011 7051278 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpnu11wohg/f1.bed -b /tmp/tmpnu11wohg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6120583 6129332 a 0 - 1 chrY 6120583 6128365 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp14nytr6d/f1.bed -b /tmp/tmp14nytr6d/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9829063 9836975 a 0 + 1 chr1 1841972 1849525 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwr_whf0v/f1.bed -b /tmp/tmpwr_whf0v/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 8531 a 0 + 1 chr1 1 8531 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0xxjv6by/f1.bed -b /tmp/tmp0xxjv6by/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8393556 8393858 a 0 - 1 chr2 9202068 9202370 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp78ot3onl/f1.bed -b /tmp/tmp78ot3onl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9689657 9692311 a 0 + 1 chr1 1 5075 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjpeygqg6/f1.bed -b /tmp/tmpjpeygqg6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5882125 5891157 a 0 - 1 chr1 7286091 7287468 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpje5bs61j/f1.bed -b /tmp/tmpje5bs61j/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5470275 5475597 a 0 - 1 chr2 3055859 3062973 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpry6q3m31/f1.bed -b /tmp/tmpry6q3m31/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9883434 9886894 a 0 + 1 chr1 9038045 9043982 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwg_x6o6r/f1.bed -b /tmp/tmpwg_x6o6r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 953 a 0 + 1 chr1 1 953 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp8pm79t4p/f1.bed -b /tmp/tmp8pm79t4p/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9540738 9547416 a 0 + 1 chr1 392769 394449 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpui2xs844/f1.bed -b /tmp/tmpui2xs844/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4017660 4026210 a 0 + 1 chr1 5151935 5156071 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpfpc64wkm/f1.bed -b /tmp/tmpfpc64wkm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4735167 4744297 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp7m3wc6wt/f1.bed -b /tmp/tmp7m3wc6wt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 4635 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp21htt13g/f1.bed -b /tmp/tmp21htt13g/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5716169 5722075 a 0 + 1 chrX 3926084 3931886 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpi03a51ib/f1.bed -b /tmp/tmpi03a51ib/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 1821 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpa2gb0n5i/f1.bed -b /tmp/tmpa2gb0n5i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 7775 a 0 - 1 chr1 6712840 6714874 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp08lopgn9/f1.bed -b /tmp/tmp08lopgn9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3061059 3069573 a 0 + 1 chr8 1 7 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpt_d95zd0/f1.bed -b /tmp/tmpt_d95zd0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2408 a 0 + 1 chr1 1 2408 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2viw6xzx/f1.bed -b /tmp/tmp2viw6xzx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 885619 888446 a 0 - 1 chr21 6099440 6107480 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpc4nvm0o0/f1.bed -b /tmp/tmpc4nvm0o0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6958980 6959484 a 0 + 1 chr1 4656831 4662173 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphut3s49s/f1.bed -b /tmp/tmphut3s49s/f2.bed Chromosome Start End Name Score Strand 0 chr1 2032 2033 a 0 - 1 chr1 2032 2033 a 0 - Chromosome Start End Name Score Strand 0 chr1 2725454 2734261 a 0 - 1 chr20 8763543 8765793 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpf2_icowo/f1.bed -b /tmp/tmpf2_icowo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6958980 6959484 a 0 + 1 chr1 4656831 4662173 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmps1oc4_mm/f1.bed -b /tmp/tmps1oc4_mm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3693530 3698911 a 0 + 1 chr1 9822421 9822972 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp6137g5zp/f1.bed -b /tmp/tmp6137g5zp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5470275 5475597 a 0 - 1 chr2 3055859 3062973 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjdgkbdqu/f1.bed -b /tmp/tmpjdgkbdqu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9689657 9692311 a 0 + 1 chr1 1 5075 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpy1uxntdz/f1.bed -b /tmp/tmpy1uxntdz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 953 a 0 + 1 chr1 1 953 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpxs1f5ozv/f1.bed -b /tmp/tmpxs1f5ozv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 7569 a 0 + 1 chr1 1 7569 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpc9e5c5kw/f1.bed -b /tmp/tmpc9e5c5kw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3cuff6d8/f1.bed -b /tmp/tmp3cuff6d8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6958980 6959484 a 0 + 1 chr1 4656831 4662173 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpgvpw0yee/f1.bed -b /tmp/tmpgvpw0yee/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 9347 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9u9z1qgw/f1.bed -b /tmp/tmp9u9z1qgw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3924613 3924754 a 0 + 1 chr18 9548795 9549281 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp1fd0hrwj/f1.bed -b /tmp/tmp1fd0hrwj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 647853 655510 a 0 + 1 chr1 4940147 4949497 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpbtuyy_91/f1.bed -b /tmp/tmpbtuyy_91/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 1758 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp5healbrt/f1.bed -b /tmp/tmp5healbrt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9189260 9197521 a 0 + 1 chr3 9362207 9362925 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkqvpjee8/f1.bed -b /tmp/tmpkqvpjee8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 8193 a 0 - 1 chr1 1 8193 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp__j9hbof/f1.bed -b /tmp/tmp__j9hbof/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5646340 5648597 a 0 + 1 chr1 5646340 5654367 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpq8ta0iuf/f1.bed -b /tmp/tmpq8ta0iuf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 7775 a 0 - 1 chr1 6712840 6714874 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4asqguw4/f1.bed -b /tmp/tmp4asqguw4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 10001 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpa5cvidug/f1.bed -b /tmp/tmpa5cvidug/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 8555 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp1rsnjzfo/f1.bed -b /tmp/tmp1rsnjzfo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9859847 9867358 a 0 + 1 chr13 8502689 8512688 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwa9f34w2/f1.bed -b /tmp/tmpwa9f34w2/f2.bed Chromosome Start End Name Score Strand 0 chr1 7216 7217 a 0 - 1 chr1 7216 7217 a 0 - Chromosome Start End Name Score Strand 0 chr1 2561070 2566062 a 0 + 1 chr1 4222690 4229384 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpgvwalhyw/f1.bed -b /tmp/tmpgvwalhyw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3061059 3069573 a 0 + 1 chr8 1 7 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_0_p58tp/f1.bed -b /tmp/tmp_0_p58tp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 9347 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjc_vey8g/f1.bed -b /tmp/tmpjc_vey8g/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 1766 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpuofrp8i7/f1.bed -b /tmp/tmpuofrp8i7/f2.bed Chromosome Start End Name Score Strand 0 chr1 3980 3981 a 0 - 1 chr1 3980 3981 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 10001 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpibfr8ysq/f1.bed -b /tmp/tmpibfr8ysq/f2.bed Chromosome Start End Name Score Strand 0 chr13 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2909437 2918999 a 0 - 1 chr10 2740846 2746147 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpcgx3txjt/f1.bed -b /tmp/tmpcgx3txjt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6466510 6468837 a 0 + 1 chr8 8105639 8105640 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpgoej4jsw/f1.bed -b /tmp/tmpgoej4jsw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 631196 632719 a 0 - 1 chr8 631196 635292 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp5nou6grw/f1.bed -b /tmp/tmp5nou6grw/f2.bed Chromosome Start End Name Score Strand 0 chr1 7216 7217 a 0 - 1 chr1 7216 7217 a 0 - Chromosome Start End Name Score Strand 0 chr1 5646340 5648597 a 0 + 1 chr1 5646340 5654367 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0izs6o6v/f1.bed -b /tmp/tmp0izs6o6v/f2.bed Chromosome Start End Name Score Strand 0 chr1 569 570 a 0 - 1 chr1 569 570 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 842 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpmma5vnfw/f1.bed -b /tmp/tmpmma5vnfw/f2.bed Chromosome Start End Name Score Strand 0 chr1 5115 5116 a 0 - 1 chr1 5115 5116 a 0 - Chromosome Start End Name Score Strand 0 chr1 3006660 3014542 a 0 - 1 chr2 3543829 3550101 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmprdowvmjt/f1.bed -b /tmp/tmprdowvmjt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2408 a 0 + 1 chr1 1 2408 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpi2qpiqnu/f1.bed -b /tmp/tmpi2qpiqnu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9901168 9903249 a 0 + 1 chr1 3949680 3952206 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpdf44iimy/f1.bed -b /tmp/tmpdf44iimy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4505494 4511395 a 0 + 1 chr2 3454041 3459747 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpe0whgxp8/f1.bed -b /tmp/tmpe0whgxp8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 6895 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqq7lztwm/f1.bed -b /tmp/tmpqq7lztwm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 842 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpalkgdosf/f1.bed -b /tmp/tmpalkgdosf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3935951 3942709 a 0 + 1 chr1 6396945 6406275 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpj0sodi2f/f1.bed -b /tmp/tmpj0sodi2f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 9948 a 0 + 1 chr18 7044011 7051278 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvp72dgaa/f1.bed -b /tmp/tmpvp72dgaa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4627406 4633713 a 0 - 1 chr1 9766914 9772319 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpo47mf5wr/f1.bed -b /tmp/tmpo47mf5wr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7302688 7310597 a 0 + 1 chr1 9806145 9807940 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp30543l9g/f1.bed -b /tmp/tmp30543l9g/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9718579 9723050 a 0 - 1 chr18 2111180 2113014 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvynpgvw5/f1.bed -b /tmp/tmpvynpgvw5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9901168 9903249 a 0 + 1 chr1 3949680 3952206 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpei5xwt2r/f1.bed -b /tmp/tmpei5xwt2r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4505494 4511395 a 0 + 1 chr2 3454041 3459747 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpc5lqbxxm/f1.bed -b /tmp/tmpc5lqbxxm/f2.bed Chromosome Start End Name Score Strand 0 chr13 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4505494 4511395 a 0 + 1 chr2 3454041 3459747 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2uc26v90/f1.bed -b /tmp/tmp2uc26v90/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6466510 6468837 a 0 + 1 chr8 8105639 8105640 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp_w663z9u/f1.bed -b /tmp/tmp_w663z9u/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpzzzt_w9e/f1.bed -b /tmp/tmpzzzt_w9e/f2.bed Chromosome Start End Name Score Strand 0 chr1 2327 2328 a 0 - 1 chr1 2327 2328 a 0 - Chromosome Start End Name Score Strand 0 chr1 7825316 7835264 a 0 - 1 chrX 2112798 2116618 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpe47z7i68/f1.bed -b /tmp/tmpe47z7i68/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4735167 4744297 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpqple8ozx/f1.bed -b /tmp/tmpqple8ozx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 5206 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpd9w2yfm3/f1.bed -b /tmp/tmpd9w2yfm3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 8962 a 0 - 1 chr1 1 8962 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpejoi43wa/f1.bed -b /tmp/tmpejoi43wa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2236425 2244451 a 0 + 1 chr1 2 7811 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpl00ckv82/f1.bed -b /tmp/tmpl00ckv82/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9859847 9867358 a 0 + 1 chr13 8502689 8512688 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpgdpxj5g1/f1.bed -b /tmp/tmpgdpxj5g1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6083007 6084297 a 0 + 1 chr1 433328 434618 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpp99rt57n/f1.bed -b /tmp/tmpp99rt57n/f2.bed Chromosome Start End Name Score Strand 0 chr1 3980 3981 a 0 - 1 chr1 3980 3981 a 0 - Chromosome Start End Name Score Strand 0 chr1 631196 632719 a 0 - 1 chr8 631196 635292 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpown0onnt/f1.bed -b /tmp/tmpown0onnt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 384754 391376 a 0 + 1 chr1 2708870 2717162 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsnharuyq/f1.bed -b /tmp/tmpsnharuyq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6466510 6468837 a 0 + 1 chr8 8105639 8105640 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpgy1u253_/f1.bed -b /tmp/tmpgy1u253_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 7569 a 0 + 1 chr1 1 7569 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpfh866yhw/f1.bed -b /tmp/tmpfh866yhw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7033220 7041111 a 0 + 1 chr1 8284506 8292327 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3qzae7fj/f1.bed -b /tmp/tmp3qzae7fj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3935951 3942709 a 0 + 1 chr1 6396945 6406275 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9n4ftodh/f1.bed -b /tmp/tmp9n4ftodh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3006660 3014542 a 0 - 1 chr2 3543829 3550101 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsz1nv2lg/f1.bed -b /tmp/tmpsz1nv2lg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6083007 6084297 a 0 + 1 chr1 433328 434618 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp1qct8pwo/f1.bed -b /tmp/tmp1qct8pwo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2687574 2689206 a 0 - 1 chr8 1341325 1350804 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp93tfjxvw/f1.bed -b /tmp/tmp93tfjxvw/f2.bed Chromosome Start End Name Score Strand 0 chr1 2327 2328 a 0 - 1 chr1 2327 2328 a 0 - Chromosome Start End Name Score Strand 0 chr1 5059809 5064224 a 0 - 1 chr13 10000000 10009403 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpb3ga0z88/f1.bed -b /tmp/tmpb3ga0z88/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5470275 5475597 a 0 - 1 chr2 3055859 3062973 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpn6la0e1s/f1.bed -b /tmp/tmpn6la0e1s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 7569 a 0 + 1 chr1 1 7569 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwgn3u81p/f1.bed -b /tmp/tmpwgn3u81p/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 10001 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpg883vdej/f1.bed -b /tmp/tmpg883vdej/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6365933 6375808 a 0 + 1 chr20 9178600 9184038 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpj4mvyzuf/f1.bed -b /tmp/tmpj4mvyzuf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7642402 7643412 a 0 + 1 chr1 4053363 4053364 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpmatmt36i/f1.bed -b /tmp/tmpmatmt36i/f2.bed Chromosome Start End Name Score Strand 0 chr1 5115 5116 a 0 - 1 chr1 5115 5116 a 0 - Chromosome Start End Name Score Strand 0 chr1 4017660 4026210 a 0 + 1 chr1 5151935 5156071 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmps6y3k4nu/f1.bed -b /tmp/tmps6y3k4nu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1780559 1784403 a 0 + 1 chr1 8707623 8714649 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp1atum5ga/f1.bed -b /tmp/tmp1atum5ga/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 7775 a 0 - 1 chr1 6712840 6714874 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpo9jg0d1u/f1.bed -b /tmp/tmpo9jg0d1u/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9594729 9601618 a 0 - 1 chr11 787164 790554 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0qpqfk_t/f1.bed -b /tmp/tmp0qpqfk_t/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1095658 1101750 a 0 + 1 chr1 1505992 1512353 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpon7xnosj/f1.bed -b /tmp/tmpon7xnosj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 7569 a 0 + 1 chr1 1 7569 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp09h2c0ob/f1.bed -b /tmp/tmp09h2c0ob/f2.bed Chromosome Start End Name Score Strand 0 chr1 5321 5322 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 842 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpo6zflhy0/f1.bed -b /tmp/tmpo6zflhy0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 1766 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpkt42bcx3/f1.bed -b /tmp/tmpkt42bcx3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2561070 2566062 a 0 + 1 chr1 4222690 4229384 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpbzr4l_tb/f1.bed -b /tmp/tmpbzr4l_tb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 5206 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2rd0t7io/f1.bed -b /tmp/tmp2rd0t7io/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4505494 4511395 a 0 + 1 chr2 3454041 3459747 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0idfp1_e/f1.bed -b /tmp/tmp0idfp1_e/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 384754 391376 a 0 + 1 chr1 2708870 2717162 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp225oqocj/f1.bed -b /tmp/tmp225oqocj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2909437 2918999 a 0 - 1 chr10 2740846 2746147 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp5c_h_d1w/f1.bed -b /tmp/tmp5c_h_d1w/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 8899 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp6egmv1ct/f1.bed -b /tmp/tmp6egmv1ct/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3924613 3924754 a 0 + 1 chr18 9548795 9549281 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpp2o_vpfr/f1.bed -b /tmp/tmpp2o_vpfr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8393556 8393858 a 0 - 1 chr2 9202068 9202370 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjc5jf1i3/f1.bed -b /tmp/tmpjc5jf1i3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4505494 4511395 a 0 + 1 chr2 3454041 3459747 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpczrvgif_/f1.bed -b /tmp/tmpczrvgif_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7033220 7041111 a 0 + 1 chr1 8284506 8292327 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpmm9f5j4c/f1.bed -b /tmp/tmpmm9f5j4c/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9999163 10004713 a 0 + 1 chr1 9926834 9929837 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp8t6qsavr/f1.bed -b /tmp/tmp8t6qsavr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 5426 a 0 + 1 chr1 1 5426 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp2rubelrh/f1.bed -b /tmp/tmp2rubelrh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2687574 2689206 a 0 - 1 chr8 1341325 1350804 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmppsbr_ka_/f1.bed -b /tmp/tmppsbr_ka_/f2.bed Chromosome Start End Name Score Strand 0 chr1 7404 7405 a 0 + Chromosome Start End Name Score Strand 0 chr1 9594729 9601618 a 0 - 1 chr11 787164 790554 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp7tqsrnlr/f1.bed -b /tmp/tmp7tqsrnlr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9689657 9692311 a 0 + 1 chr1 1 5075 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpq6vaiguf/f1.bed -b /tmp/tmpq6vaiguf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpux81pfn1/f1.bed -b /tmp/tmpux81pfn1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 7569 a 0 + 1 chr1 1 7569 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4odsg7s4/f1.bed -b /tmp/tmp4odsg7s4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2236425 2244451 a 0 + 1 chr1 2 7811 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp6n8chm62/f1.bed -b /tmp/tmp6n8chm62/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5470275 5475597 a 0 - 1 chr2 3055859 3062973 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmplepi51ko/f1.bed -b /tmp/tmplepi51ko/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 885619 888446 a 0 - 1 chr21 6099440 6107480 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp4g2lo6oa/f1.bed -b /tmp/tmp4g2lo6oa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9883434 9886894 a 0 + 1 chr1 9038045 9043982 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpmk7pusk2/f1.bed -b /tmp/tmpmk7pusk2/f2.bed Chromosome Start End Name Score Strand 0 chr1 5115 5116 a 0 - 1 chr1 5115 5116 a 0 - Chromosome Start End Name Score Strand 0 chr1 9718579 9723050 a 0 - 1 chr18 2111180 2113014 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp9rdv0310/f1.bed -b /tmp/tmp9rdv0310/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 8962 a 0 - 1 chr1 1 8962 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpmia_takq/f1.bed -b /tmp/tmpmia_takq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp11shbvaa/f1.bed -b /tmp/tmp11shbvaa/f2.bed ___________ test_three_in_a_row[strandedness_chain57-method_chain57] ___________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ____________ test_three_in_a_row[strandedness_chain2-method_chain2] ____________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 185 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') _________________ test_k_nearest[upstream-True-opposite-last] __________________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1s.values, d2e.values, d1s.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=True, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjRRRgBOKMDFg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1e.values, d2s.values, d1e.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=True, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 41 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGMEijDDEAAAx1ALW') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg9xk63hw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg9xk63hw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdv07l_g8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdv07l_g8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4x_62n_1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4x_62n_1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1bxwlsbs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1bxwlsbs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp53c4cxlo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp53c4cxlo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgscpns3x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgscpns3x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpokvo3bp0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpokvo3bp0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx8vd4ob1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx8vd4ob1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkwedxjg8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkwedxjg8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxk2vcxlp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxk2vcxlp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe75l274v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe75l274v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsl61zhot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsl61zhot/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqoewojab/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqoewojab/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqos96gfw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqos96gfw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpspqejdrv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpspqejdrv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpimwb7wsi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpimwb7wsi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmph0wrfk26/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph0wrfk26/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpepblmivd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpepblmivd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpamp7urfb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpamp7urfb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnxu9cc5l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnxu9cc5l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2zs1g4dp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2zs1g4dp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgy9pn6fb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgy9pn6fb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx5cjqr0w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx5cjqr0w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp25c1l7wv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp25c1l7wv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc2pza6af/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc2pza6af/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkeh2wbv4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkeh2wbv4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsv5gml38/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsv5gml38/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk9j50zaf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk9j50zaf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgpwx1hyf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgpwx1hyf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoe9uk5xq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoe9uk5xq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpybdjf649/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpybdjf649/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw6t8qgxu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw6t8qgxu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp44f4a49a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp44f4a49a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp20mordb0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp20mordb0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp2ire3ig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp2ire3ig/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi7jh78pg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi7jh78pg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdc02c5v6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdc02c5v6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnbzhv8mc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnbzhv8mc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprzkz_z0m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprzkz_z0m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp68dy5idz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp68dy5idz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpia1ddhjb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpia1ddhjb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuiuhaisa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuiuhaisa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2b_naput/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2b_naput/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgpfdmz4p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgpfdmz4p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdhawhdxg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdhawhdxg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpal_r5iqh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpal_r5iqh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqkmnr7e3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqkmnr7e3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprtc86x24/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprtc86x24/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpudjfp_9a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpudjfp_9a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyfa3t1zq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyfa3t1zq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfglh1gf9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfglh1gf9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqzsbb5qk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqzsbb5qk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6oj4d8sm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6oj4d8sm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8gn4elsl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8gn4elsl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyk3bk61o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyk3bk61o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0a39ym9z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0a39ym9z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu337g6h1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu337g6h1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc6j2m8w7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc6j2m8w7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprlxvnbxt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprlxvnbxt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd0iim1dl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd0iim1dl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3d11g786/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3d11g786/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw8v_sctg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw8v_sctg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ijkzjp6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ijkzjp6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyjy6v3jx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyjy6v3jx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp26bqjubf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp26bqjubf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp90bh6wsq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp90bh6wsq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjupt2o_u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjupt2o_u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpez34pkm8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpez34pkm8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9f58wd_l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9f58wd_l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpefqf9jiy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpefqf9jiy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo62imvma/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo62imvma/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpos4ha8y_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpos4ha8y_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplxriukpr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplxriukpr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp7jgcrt2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7jgcrt2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgsp___ti/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgsp___ti/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp283bhgam/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp283bhgam/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppo7i7205/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppo7i7205/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpro3xt012/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpro3xt012/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpedm349os/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpedm349os/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk57gf04p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk57gf04p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps2q3wup_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps2q3wup_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgvh_kb3n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgvh_kb3n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1z144cq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1z144cq2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmph29hraf9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph29hraf9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp42ap_ik8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp42ap_ik8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt7j9w30v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt7j9w30v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjczmbunn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjczmbunn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_prsrvbt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_prsrvbt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ojjzw33/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ojjzw33/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfgxd9haj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfgxd9haj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnyunlbxa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnyunlbxa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjegui_m3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjegui_m3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3cfbdjdb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3cfbdjdb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa816cksc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa816cksc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp02w3noq0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp02w3noq0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcoydcs3l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcoydcs3l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu0lzh8pv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu0lzh8pv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwm7ax5mo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwm7ax5mo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp40cnjt5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp40cnjt5d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpak9j5fxq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpak9j5fxq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv75640zi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv75640zi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4jr3isgd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4jr3isgd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptvdcuvtp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptvdcuvtp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpknh65vhb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpknh65vhb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgbsxbdde/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgbsxbdde/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9by472kr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9by472kr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_zmzzlad/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_zmzzlad/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzsl6065k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzsl6065k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3fyzapov/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3fyzapov/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbfqont81/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbfqont81/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9hhwb5gr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9hhwb5gr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp29_9_dy7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp29_9_dy7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2tlobizv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2tlobizv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps52h11r3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps52h11r3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp53suzmxf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp53suzmxf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjy5pym8d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjy5pym8d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz3r7cqi6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz3r7cqi6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw74q_mp1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw74q_mp1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzsl7pzm_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzsl7pzm_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl1t2vbh9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl1t2vbh9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo2m532qf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo2m532qf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3epvmya9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3epvmya9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkjyhdd9d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkjyhdd9d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc_bu0ws1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc_bu0ws1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp7ze88ct/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7ze88ct/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl_9gsvqb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl_9gsvqb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6mlz72v6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6mlz72v6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi6ctc79z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi6ctc79z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwh6dhe1n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwh6dhe1n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg7j67wu9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7j67wu9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpavlxeto_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpavlxeto_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnq5ia2e7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnq5ia2e7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptm_c0db_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptm_c0db_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5o7bs67k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5o7bs67k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwc95qliy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwc95qliy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1ccw2n26/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ccw2n26/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc0ku8tah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc0ku8tah/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpscbigqy9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpscbigqy9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxi4gekzo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxi4gekzo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk00mzsgg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk00mzsgg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoyeywjen/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoyeywjen/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2uoie81s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2uoie81s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpat78h0t4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpat78h0t4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpos5h5b5i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpos5h5b5i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9bhbwnpw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9bhbwnpw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcjp5qcz_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcjp5qcz_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6bjjttoa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6bjjttoa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb5dgs9tm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb5dgs9tm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5qrauf_7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5qrauf_7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfll3g9bp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfll3g9bp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps2kyn8ky/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps2kyn8ky/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqtq0jbud/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqtq0jbud/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8iqwffsg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8iqwffsg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps638l9vn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps638l9vn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptlbnk00q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptlbnk00q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp57o4myuo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp57o4myuo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzzi2no6k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzzi2no6k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnicva78i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnicva78i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprvi4pnwh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprvi4pnwh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp90tthap2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp90tthap2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpql3bf7lc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpql3bf7lc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1nnroy5u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1nnroy5u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnwvkhvy3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnwvkhvy3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7fixkj2u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7fixkj2u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsfniqr66/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsfniqr66/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyr99mphp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyr99mphp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2l7hu87_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2l7hu87_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6a_8cr2f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6a_8cr2f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzwfj1hiw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzwfj1hiw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcp08rxwx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcp08rxwx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprwxo_8k1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprwxo_8k1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0am57v9t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0am57v9t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkr_x6p37/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkr_x6p37/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw4wvx5z7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw4wvx5z7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptky_dl_j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptky_dl_j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_cyuxt4b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_cyuxt4b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz5pxyhjd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz5pxyhjd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj15_aytr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj15_aytr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbc6i7go3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbc6i7go3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5gnbsr2r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5gnbsr2r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1qk746kz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1qk746kz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeeta6pcb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeeta6pcb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc3t9go6f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc3t9go6f/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ____________ test_three_in_a_row[strandedness_chain9-method_chain9] ____________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 66 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges 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('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ___________ test_three_in_a_row[strandedness_chain35-method_chain35] ___________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 133 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 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('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ___________________ test_k_nearest[upstream-True-same-last] ____________________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1e.values, d2s.values, d1e.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=True, | strandedness='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 41 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGDFEADi2Axc=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1s.values, d2e.values, d1s.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=True, | strandedness='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp43mcxgfa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp43mcxgfa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4dnnmu6g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4dnnmu6g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpby5vf_m4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpby5vf_m4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxz78ahwn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxz78ahwn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxtrs1iax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxtrs1iax/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbr0mi_84/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbr0mi_84/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcapywwu9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcapywwu9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpox07oqrz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpox07oqrz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf_d69wh8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf_d69wh8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwrczy606/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwrczy606/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpra3urppo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpra3urppo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxy4a1sbw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxy4a1sbw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcmwpl7qj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcmwpl7qj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmi2a6d34/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmi2a6d34/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6p0yn8yq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6p0yn8yq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8dpmm46j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8dpmm46j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdvtqtrvx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdvtqtrvx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgxk038se/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgxk038se/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1bs994mj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1bs994mj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvgx97jam/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvgx97jam/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoaem5px5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoaem5px5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmps31th2ls/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps31th2ls/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpleymro2r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpleymro2r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxvk6vs16/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxvk6vs16/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0n6_ewx_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0n6_ewx_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv7djrh2f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv7djrh2f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqkrpfjrs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqkrpfjrs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwkyvd6nr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwkyvd6nr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaeb_josi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaeb_josi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfq2a2wmp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfq2a2wmp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdzwp4pco/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdzwp4pco/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuc0hl8y7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuc0hl8y7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_aygqkbn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_aygqkbn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv2mxi1d6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv2mxi1d6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbc_k4lh_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbc_k4lh_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpktjfrppg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpktjfrppg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj4x64zxt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj4x64zxt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn3btoi3g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn3btoi3g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgnuygadh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgnuygadh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvtqwe59a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtqwe59a/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain21-method_chain21] ___________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 168 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 360, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | (and 282 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 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'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________ test_three_in_a_row[strandedness_chain3-method_chain3] ____________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 177 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ___________ test_three_in_a_row[strandedness_chain49-method_chain49] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 221 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ___________ test_three_in_a_row[strandedness_chain10-method_chain10] ___________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E /usr/lib/python3/dist-packages/pandas/core/common.py:143 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ___________ test_three_in_a_row[strandedness_chain58-method_chain58] ___________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') _____________________ test_nearest[upstream-True-opposite] _____________________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.End) | ^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 127 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEJGIMEEZDKC2VBBMBeEAELMA1k=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.Start, ocdf.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_ends.values - 1, right_starts.values, right_indexes) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 127 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEJGIMEEZDICESNYkBGGGAA7dwMZ') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | ~~~~~~~~~~~~~~~~~~~^ | lcol, | ^^^^^ | ...<12 lines>... | check_flags=False, | ^^^^^^^^^^^^^^^^^^ | ) | ^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 466 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGMEijDDEAAAx1ALW') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxnbnzib4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxnbnzib4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_jr2rg14/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_jr2rg14/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp31dd961g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp31dd961g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppm0onhyo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppm0onhyo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmporcpo2wf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmporcpo2wf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu2uxtuj3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu2uxtuj3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprs2uq2vr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprs2uq2vr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpudtkwl9y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpudtkwl9y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0_k5hq2q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_k5hq2q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptev5s9w5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptev5s9w5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyo_gjgg4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyo_gjgg4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpobkxi44d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpobkxi44d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm1fwok2t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm1fwok2t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc2xqyhqr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc2xqyhqr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn42e0ead/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn42e0ead/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt2vy6bcz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt2vy6bcz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfj_k50n0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfj_k50n0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpps67mo56/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpps67mo56/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv6ckjl8g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv6ckjl8g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplzfn2596/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplzfn2596/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpinx4hpzs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpinx4hpzs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4yvajb7z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4yvajb7z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp46z4gsjh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp46z4gsjh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj_rpctx5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj_rpctx5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy423s8xm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy423s8xm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwe43ebrd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwe43ebrd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptghhwd0p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptghhwd0p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfzwhoyg3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfzwhoyg3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfw00alyt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfw00alyt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1qb0cbcv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1qb0cbcv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9cv5_gut/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9cv5_gut/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1qcbcda5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1qcbcda5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpathsfnwe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpathsfnwe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp58p0ollc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp58p0ollc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfpqedjkx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfpqedjkx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa9l1vqfa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa9l1vqfa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0tz4tolb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0tz4tolb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsofh967v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsofh967v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwp7cktj_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwp7cktj_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr5mzrf0a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr5mzrf0a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj4hebwjw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj4hebwjw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx7od8rad/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx7od8rad/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppmr73jar/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppmr73jar/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcrjlh8ep/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcrjlh8ep/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp00ozkf08/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00ozkf08/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprvbqeile/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprvbqeile/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp54dyf1wt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp54dyf1wt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_7kf04s7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7kf04s7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeptldq3e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeptldq3e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmposmuzhrw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmposmuzhrw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5_nnn827/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5_nnn827/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz9eij989/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz9eij989/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp241ozsv9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp241ozsv9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp79yx4sls/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp79yx4sls/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwarfkep0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwarfkep0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkoj1o0rh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkoj1o0rh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3zwdsmur/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3zwdsmur/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdxbm1j2i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdxbm1j2i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm5wrjbnu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm5wrjbnu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplbhh1805/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplbhh1805/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdhw81r4w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdhw81r4w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpit_9ma2n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpit_9ma2n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphzbz19r5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphzbz19r5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkw4p0sl6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkw4p0sl6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpokk17ior/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpokk17ior/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr14 1 2 - 0 3 chr14 1 2 - 0 4 chr14 1 2 - 0 5 chr14 1 2806 + 0 6 chr14 1 313 + 0 7 chr14 1 4468 + 0 8 chr14 1 5343 - 0 9 chr14 1 6381 - 0 10 chr14 1 7490 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr14 | 1 | 4468 | a | 0 | ... | | chr14 | 1 | 313 | a | 0 | ... | | chr14 | 1 | 2806 | a | 0 | ... | | chr14 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr14 | 1 | 2 | a | 0 | ... | | chr14 | 1 | 6381 | a | 0 | ... | | chr14 | 1 | 7490 | a | 0 | ... | | chr14 | 1 | 5343 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr14 1 2 - 0 4 chr14 1 2 - 0 5 chr14 1 2 - 0 1 chr14 1 313 + 0 2 chr14 1 2806 + 0 0 chr14 1 4468 + 0 8 chr14 1 5343 - 0 6 chr14 1 6381 - 0 7 chr14 1 7490 - 0 df2 Chromosome Start End Strand Distance 2 chr14 1 2 - 0 3 chr14 1 2 - 0 4 chr14 1 2 - 0 6 chr14 1 313 + 0 5 chr14 1 2806 + 0 7 chr14 1 4468 + 0 8 chr14 1 5343 - 0 9 chr14 1 6381 - 0 10 chr14 1 7490 - 0 Actual Chromosome Start End Strand Distance 0 chr14 1 2 - 0 1 chr14 1 2 - 0 2 chr14 1 2 - 0 3 chr14 1 313 + 0 4 chr14 1 2806 + 0 5 chr14 1 4468 + 0 6 chr14 1 5343 - 0 7 chr14 1 6381 - 0 8 chr14 1 7490 - 0 Expected Chromosome Start End Strand Distance 0 chr14 1 2 - 0 1 chr14 1 2 - 0 2 chr14 1 2 - 0 3 chr14 1 313 + 0 4 chr14 1 2806 + 0 5 chr14 1 4468 + 0 6 chr14 1 5343 - 0 7 chr14 1 6381 - 0 8 chr14 1 7490 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaka8h5jk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaka8h5jk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4qte6owp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4qte6owp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr14 1 2 - 0 3 chr14 1 2 - 0 4 chr14 1 2 - 0 5 chr14 1 2806 + 0 6 chr14 1 313 + 0 7 chr14 1 4468 + 0 8 chr14 1 5343 - 0 9 chr14 1 6381 - 0 10 chr14 1 7490 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr14 | 1 | 4468 | a | 0 | ... | | chr14 | 1 | 313 | a | 0 | ... | | chr14 | 1 | 2806 | a | 0 | ... | | chr14 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr14 | 1 | 2 | a | 0 | ... | | chr14 | 1 | 6381 | a | 0 | ... | | chr14 | 1 | 7490 | a | 0 | ... | | chr14 | 1 | 5343 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr14 1 2 - 0 4 chr14 1 2 - 0 5 chr14 1 2 - 0 1 chr14 1 313 + 0 2 chr14 1 2806 + 0 0 chr14 1 4468 + 0 8 chr14 1 5343 - 0 6 chr14 1 6381 - 0 7 chr14 1 7490 - 0 df2 Chromosome Start End Strand Distance 2 chr14 1 2 - 0 3 chr14 1 2 - 0 4 chr14 1 2 - 0 6 chr14 1 313 + 0 5 chr14 1 2806 + 0 7 chr14 1 4468 + 0 8 chr14 1 5343 - 0 9 chr14 1 6381 - 0 10 chr14 1 7490 - 0 Actual Chromosome Start End Strand Distance 0 chr14 1 2 - 0 1 chr14 1 2 - 0 2 chr14 1 2 - 0 3 chr14 1 313 + 0 4 chr14 1 2806 + 0 5 chr14 1 4468 + 0 6 chr14 1 5343 - 0 7 chr14 1 6381 - 0 8 chr14 1 7490 - 0 Expected Chromosome Start End Strand Distance 0 chr14 1 2 - 0 1 chr14 1 2 - 0 2 chr14 1 2 - 0 3 chr14 1 313 + 0 4 chr14 1 2806 + 0 5 chr14 1 4468 + 0 6 chr14 1 5343 - 0 7 chr14 1 6381 - 0 8 chr14 1 7490 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzvzbl2z6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzvzbl2z6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbfu526gt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbfu526gt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdr0ewty6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdr0ewty6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfla8qwtv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfla8qwtv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfa3msw5h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfa3msw5h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppy2rd_ly/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppy2rd_ly/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphmuwqwmv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphmuwqwmv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi103kkx3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi103kkx3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp142pgw8n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp142pgw8n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprire3rba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprire3rba/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ilm4qlt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ilm4qlt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp7pmv8c1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7pmv8c1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj8r9k34_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj8r9k34_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp38eenk1m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp38eenk1m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5197x0qj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5197x0qj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpofch_2u8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpofch_2u8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc8lt3tp1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc8lt3tp1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprjzzyg2g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprjzzyg2g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpur6i_oi7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpur6i_oi7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphcayibhl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphcayibhl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy74mudbx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy74mudbx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxfpoz7t4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxfpoz7t4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn8fwvc6x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn8fwvc6x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0byx9nqf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0byx9nqf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0x_loie5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0x_loie5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppcivaxvm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppcivaxvm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpytzs6xsr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpytzs6xsr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgq1w_l_v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgq1w_l_v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi3r4gpt0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi3r4gpt0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphtjfr9e3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphtjfr9e3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4z7jceyh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4z7jceyh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp804snp1m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp804snp1m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpafmd8k7z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpafmd8k7z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxcm2p6t7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxcm2p6t7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_lw37yld/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_lw37yld/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxthm_cns/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxthm_cns/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5fxwr25w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5fxwr25w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_utsj7q7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_utsj7q7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa8934vgf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa8934vgf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqvj_3hgt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqvj_3hgt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf16og5fs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf16og5fs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9zzvr26r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9zzvr26r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpza6eze63/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpza6eze63/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0r4a1eyi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0r4a1eyi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphnehty6t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphnehty6t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_5srg8y3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_5srg8y3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpepbypxgv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpepbypxgv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 1 4062 - 0 2 chr1 1 4855 - 0 4 chr1 1 5973 - 0 6 chr1 1 6311 - 0 7 chr1 1 7492 - 0 8 chr1 1 7779 - 0 9 chr1 1 8715 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 8715 | a | 0 | ... | | chr1 | 1 | 7779 | a | 0 | ... | | chr1 | 1 | 4062 | a | 0 | ... | | chr1 | 1 | 7492 | a | 0 | ... | | chr1 | 1 | 6311 | a | 0 | ... | | chr1 | 1 | 4855 | a | 0 | ... | | chr1 | 1 | 5973 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 4062 - 0 5 chr1 1 4855 - 0 6 chr1 1 5973 - 0 4 chr1 1 6311 - 0 3 chr1 1 7492 - 0 1 chr1 1 7779 - 0 0 chr1 1 8715 - 0 df2 Chromosome Start End Strand Distance 1 chr1 1 4062 - 0 2 chr1 1 4855 - 0 4 chr1 1 5973 - 0 6 chr1 1 6311 - 0 7 chr1 1 7492 - 0 8 chr1 1 7779 - 0 9 chr1 1 8715 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 4062 - 0 1 chr1 1 4855 - 0 2 chr1 1 5973 - 0 3 chr1 1 6311 - 0 4 chr1 1 7492 - 0 5 chr1 1 7779 - 0 6 chr1 1 8715 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 4062 - 0 1 chr1 1 4855 - 0 2 chr1 1 5973 - 0 3 chr1 1 6311 - 0 4 chr1 1 7492 - 0 5 chr1 1 7779 - 0 6 chr1 1 8715 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1qob9r9l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1qob9r9l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzv8i6ft0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzv8i6ft0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprpsly4m6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprpsly4m6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp864lpu1m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp864lpu1m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfy4dz7kz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfy4dz7kz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsjyz41_4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsjyz41_4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8xyo9xzt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8xyo9xzt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk_8cico6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_8cico6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx3jdo26d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3jdo26d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppqxeft8t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppqxeft8t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqad8ereg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqad8ereg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnd7gbojy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnd7gbojy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpemcp3lbj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpemcp3lbj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpngmok2oz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpngmok2oz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp13rrm3jq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp13rrm3jq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0_yiduf6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_yiduf6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgz78q35f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgz78q35f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp16qeq1_p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp16qeq1_p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7exiidr2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7exiidr2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqnpxujcv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqnpxujcv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvn_8z_ou/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvn_8z_ou/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpehhgp4et/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpehhgp4et/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptn2zux6v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptn2zux6v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1270u2w3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1270u2w3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxpfg54p_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxpfg54p_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkng_8cn2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkng_8cn2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbjgdqd63/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbjgdqd63/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0u486av6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0u486av6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5rmnz7r1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5rmnz7r1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpte7ouuih/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpte7ouuih/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo76fwuhj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo76fwuhj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyf3jam9z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyf3jam9z/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphqxme6kw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphqxme6kw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa8ybfhq0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa8ybfhq0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4f_6999a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4f_6999a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb06om_s0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb06om_s0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphtnt_ij9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphtnt_ij9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp555iazf6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp555iazf6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwsluibq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwsluibq2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_dezyjnq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_dezyjnq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa7yzkwal/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa7yzkwal/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv9qykekj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv9qykekj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo70beab9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo70beab9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppxj6pyy0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppxj6pyy0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu_aqzvcm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu_aqzvcm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe23ciq6p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe23ciq6p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpllcrgvxl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpllcrgvxl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoc2xctcu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoc2xctcu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp39_7sj9h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp39_7sj9h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7re3mzx2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7re3mzx2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmycxj5jd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmycxj5jd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzft9t3de/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzft9t3de/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp140o0ca9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp140o0ca9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe6mk1ylh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe6mk1ylh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp067lm9ob/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp067lm9ob/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpst35uozq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpst35uozq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplx1dn8zr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplx1dn8zr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpse6twrw3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpse6twrw3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0npbep05/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0npbep05/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkrt6p442/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkrt6p442/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc51pbpkm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc51pbpkm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6zw6vz9s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6zw6vz9s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbr6m9he6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbr6m9he6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa7n366dz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa7n366dz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9bvrcknd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9bvrcknd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7s2pqzym/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7s2pqzym/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwb4nmn9m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwb4nmn9m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb0fy_eed/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb0fy_eed/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn31n5ynf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn31n5ynf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0_p5t4wv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_p5t4wv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqbh3fvoa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqbh3fvoa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjzzfgp2r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjzzfgp2r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1x1vr9q2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1x1vr9q2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzlfzsfpu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzlfzsfpu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgdl_zo7r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgdl_zo7r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv21z7ybx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv21z7ybx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoointeyq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoointeyq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp69lkb_o6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp69lkb_o6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzyqgacza/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzyqgacza/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpil4k218u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpil4k218u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbxvoitzz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbxvoitzz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_hpold2d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_hpold2d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3ipt57l3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ipt57l3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp1ge4bti/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp1ge4bti/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5ojnlsng/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ojnlsng/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprorlhd3x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprorlhd3x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgvlvn5oc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgvlvn5oc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_voztdzc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_voztdzc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoxxygdmn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoxxygdmn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplmnnej_q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplmnnej_q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk80dvhy2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk80dvhy2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl10o8v18/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl10o8v18/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaaqu44wv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaaqu44wv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpic3f1ub4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpic3f1ub4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp32d4elxx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp32d4elxx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkvk9ugp4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkvk9ugp4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppc4a3__5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppc4a3__5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaaq7royw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaaq7royw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr22 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr22 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr22 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr22 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr22 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr22 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa41gzj9u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa41gzj9u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxv7rx3v5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxv7rx3v5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr22 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr22 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr22 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr22 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr22 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr22 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9i8nugsu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9i8nugsu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu6nphorj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu6nphorj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvf_d285y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvf_d285y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7bq3d7zd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7bq3d7zd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptrkfgxtc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptrkfgxtc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2mabzo18/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2mabzo18/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmputpzo0co/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmputpzo0co/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1uda1w94/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1uda1w94/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphyjvizme/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphyjvizme/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphb2w984i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphb2w984i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvzeseka2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvzeseka2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwqr61f8p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwqr61f8p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpss93xd8a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpss93xd8a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppwaziuuo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppwaziuuo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgxnm0kto/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgxnm0kto/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphgmll9ru/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphgmll9ru/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpizs43ora/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpizs43ora/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps0cmvms7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps0cmvms7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpujczmi99/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpujczmi99/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8h3zc5pm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8h3zc5pm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2m6lb24o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2m6lb24o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu3rtku0a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu3rtku0a/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1ac28y0o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ac28y0o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_hc8sa4_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_hc8sa4_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyoufel6h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyoufel6h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp464x8zmi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp464x8zmi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5bfougeq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5bfougeq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa6w614oe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa6w614oe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpas10c9x1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpas10c9x1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy96e2ejo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy96e2ejo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjdgf757b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjdgf757b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprmi4jt7o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprmi4jt7o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmi6zs2hm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmi6zs2hm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnhw7gv92/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnhw7gv92/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpufdura5i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpufdura5i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptzria94b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptzria94b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphjn_sgze/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphjn_sgze/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxfcyj0mk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxfcyj0mk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1lnnf4cw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1lnnf4cw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl02022gc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl02022gc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbpag2k3r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbpag2k3r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5v17nwqg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5v17nwqg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptc4oorki/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptc4oorki/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp20s2eder/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp20s2eder/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe7hsgiu1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7hsgiu1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoeb0v2vu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoeb0v2vu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpku4tyla9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpku4tyla9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxxn4q5wf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxxn4q5wf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmoz6t97e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmoz6t97e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj0i0ca7f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj0i0ca7f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuyugg7ha/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuyugg7ha/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdk6vp9gi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdk6vp9gi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3zailbdy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3zailbdy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmnzbz_xg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmnzbz_xg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0kf05gve/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0kf05gve/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6cv5soe8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6cv5soe8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp611ejosm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp611ejosm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7qkseb63/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qkseb63/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9l8o8iha/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9l8o8iha/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphnm2kand/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphnm2kand/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9c32iov6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9c32iov6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr5c60n_q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr5c60n_q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsb6suv7t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsb6suv7t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo365qvcd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo365qvcd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn4p9u2ox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn4p9u2ox/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptgmigjl6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptgmigjl6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd588er7s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd588er7s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2s2yx5sg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2s2yx5sg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyltm6xc0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyltm6xc0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoexa4zsj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoexa4zsj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0_1lw665/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_1lw665/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdheug3_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdheug3_x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqkvbusx2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqkvbusx2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuscoarey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuscoarey/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvynxclrv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvynxclrv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt7g5hr6p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt7g5hr6p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjmjd27lm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjmjd27lm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_xoc29pu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_xoc29pu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpchjycq85/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpchjycq85/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv38h3uf4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv38h3uf4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphl24y7sg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphl24y7sg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5aju_2p3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5aju_2p3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplv8bm0qm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplv8bm0qm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq6zhx4gi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq6zhx4gi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphqo7c9bb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphqo7c9bb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2dey5hn_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2dey5hn_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp32q0ief/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp32q0ief/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyu0vhxtc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyu0vhxtc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqrsf49fb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqrsf49fb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqe33zmhb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqe33zmhb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp7lpiagy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7lpiagy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwdy4q90v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwdy4q90v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnmhakuv5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnmhakuv5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphz1fob7t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphz1fob7t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw3t6j_1n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw3t6j_1n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5fms22tx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5fms22tx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1db2wqw3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1db2wqw3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ehmd29c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ehmd29c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4tudshil/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4tudshil/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa24kwlqs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa24kwlqs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp487vu2cd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp487vu2cd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7zfrypdo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7zfrypdo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmxx5h2eg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmxx5h2eg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyrloq0nb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyrloq0nb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbva7g8tf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbva7g8tf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgi2i4aia/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgi2i4aia/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvfjsouup/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvfjsouup/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpembs12lq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpembs12lq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpey9pwba4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpey9pwba4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8r922bun/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8r922bun/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr8v4enu9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr8v4enu9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1cwy0p5j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1cwy0p5j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpom446btx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpom446btx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdkw3g7vm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdkw3g7vm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp15ql4r11/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp15ql4r11/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5zun4h88/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5zun4h88/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmhc9w23q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmhc9w23q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnyt8vkd4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnyt8vkd4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp30hv_rp5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp30hv_rp5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp04alq_kn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp04alq_kn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyd_ls515/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyd_ls515/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdhov1gu4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdhov1gu4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpli8arpf3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpli8arpf3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp18x19qij/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp18x19qij/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_tlzhnym/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_tlzhnym/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpasvn_zty/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpasvn_zty/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp43inqkef/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp43inqkef/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1bfbcv23/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1bfbcv23/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpesixv_af/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpesixv_af/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnp4dnbra/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnp4dnbra/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptl9qef3t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptl9qef3t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgvpg9kgs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgvpg9kgs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfroyq_i1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfroyq_i1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2ww0p7uo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ww0p7uo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqqxdhtv1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqqxdhtv1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsgvpr_q3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsgvpr_q3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg8r35ev6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg8r35ev6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmped0n8yln/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmped0n8yln/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8cbx1qxf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8cbx1qxf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5cof2_dr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5cof2_dr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp62s1po9f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp62s1po9f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvhueh0h5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvhueh0h5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp05smpht2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp05smpht2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj5919ujn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5919ujn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg23fnfj_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg23fnfj_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpumo9ccfv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpumo9ccfv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9950vob6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9950vob6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiw86b23w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiw86b23w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz0n_0th5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz0n_0th5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm0wdryoj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm0wdryoj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyirtlwxb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyirtlwxb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp83x58k6u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp83x58k6u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpusss3s3o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpusss3s3o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpveeqn532/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpveeqn532/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5j_eeifs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5j_eeifs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpodafaq_a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpodafaq_a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps9zfn854/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps9zfn854/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoopq9eg3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoopq9eg3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfvgv3l8v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfvgv3l8v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppw5rurl4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppw5rurl4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvkp9doqr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvkp9doqr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpac2fkt_g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpac2fkt_g/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgcu4f1km/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgcu4f1km/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmsmd0z44/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmsmd0z44/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj9mhlpg_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj9mhlpg_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ___________ test_three_in_a_row[strandedness_chain36-method_chain36] ___________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False) method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E (and 119 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ____________ test_three_in_a_row[strandedness_chain4-method_chain4] ____________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 178 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ___________________________ test_set_intersect[same] ___________________________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:113: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:128: in test_set_intersect result = gr.set_intersect(gr2, strandedness=strandedness) pyranges/pyranges.py:3687: in set_intersect self_clusters = self.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_set_intersect( E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3SWNXdnYHBkhCEGRiCJzAcAPT0DMQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpuo8w0ue8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuo8w0ue8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpt32606bt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpt32606bt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgzvmbljf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgzvmbljf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzpd9cfsl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzpd9cfsl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvhi37ea3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvhi37ea3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpz8ewpnnr/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpz8ewpnnr/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnre0r9n6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnre0r9n6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpe84fhcyi/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe84fhcyi/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp11ek1chl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp11ek1chl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptjkkgkff/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptjkkgkff/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpextp2ygd/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpextp2ygd/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbbs40ny5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbbs40ny5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppoc94td2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppoc94td2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpql_vuhwv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpql_vuhwv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmj4_0h8b/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmj4_0h8b/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpo9f67tb9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo9f67tb9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkyiosh2s/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkyiosh2s/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp10tl4xv1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp10tl4xv1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptfrzqey2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptfrzqey2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpm6f6a0c8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm6f6a0c8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdqgnih2y/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdqgnih2y/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp95cvrzca/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp95cvrzca/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp67kqpl4u/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp67kqpl4u/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgxt4nm87/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgxt4nm87/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7a65ikto/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7a65ikto/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9bzdrvxt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9bzdrvxt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1k355amq/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1k355amq/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqhk_vh67/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqhk_vh67/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0z0suffw/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0z0suffw/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpj08l68j1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpj08l68j1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpinw9ls8k/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpinw9ls8k/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_woz4q31/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_woz4q31/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpm4po_vdo/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm4po_vdo/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8mtfs_gv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8mtfs_gv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1954817_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1954817_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4ue33aca/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4ue33aca/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpifmycz_u/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpifmycz_u/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpy88vmtdr/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpy88vmtdr/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpt297n70u/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpt297n70u/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpoob9ptkn/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpoob9ptkn/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptr_uu3qi/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptr_uu3qi/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmprmy95c4b/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprmy95c4b/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzo33vax4/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzo33vax4/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2fsgs4ng/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2fsgs4ng/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9q16bok7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9q16bok7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbjrt62wc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbjrt62wc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqfomi97l/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqfomi97l/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplb_4et78/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplb_4et78/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpf86v_qt0/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf86v_qt0/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp75cy610k/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp75cy610k/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp__4s8hrl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp__4s8hrl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkngmr_nv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkngmr_nv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpoier37x0/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpoier37x0/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdfyc9vc1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdfyc9vc1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3d964l_m/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3d964l_m/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmzt960of/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmzt960of/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvonlpn2a/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvonlpn2a/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_0hk5r3k/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_0hk5r3k/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4e91_kl3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4e91_kl3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphff3izot/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphff3izot/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2m_yiokg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2m_yiokg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdr11ef3o/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdr11ef3o/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8tsghrla/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8tsghrla/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8l6jv6dg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8l6jv6dg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_is1nc21/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_is1nc21/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbbl30753/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbbl30753/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp80040krg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp80040krg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4vop3o4l/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4vop3o4l/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplopbou9t/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplopbou9t/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpcdl4ppdx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcdl4ppdx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmprixr9e7q/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprixr9e7q/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3ikx9cro/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3ikx9cro/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppfh6m7u3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppfh6m7u3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8qdsjao_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8qdsjao_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjlf42hr2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjlf42hr2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp986ocw2v/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp986ocw2v/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptrk9jgki/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptrk9jgki/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6qvddlew/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6qvddlew/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8ftnzt8i/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8ftnzt8i/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpg4swcywq/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpg4swcywq/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0bff3dti/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0bff3dti/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgp0f6b59/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgp0f6b59/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2bg_0hx3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2bg_0hx3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpr80bn5z7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpr80bn5z7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7fdn13p1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7fdn13p1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpm5idkee_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm5idkee_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwuaaupp1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwuaaupp1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp92008105/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp92008105/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5fr21a82/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5fr21a82/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgv1df8rc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgv1df8rc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpx16n799p/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx16n799p/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmprkkd8wdw/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprkkd8wdw/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_lud02p_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_lud02p_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfduf79s3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfduf79s3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpe7jw2hj3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe7jw2hj3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3xlxz70n/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3xlxz70n/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppplpeg32/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppplpeg32/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppn_digyg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppn_digyg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpx4wee7u0/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx4wee7u0/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpiviwyqre/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpiviwyqre/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3n0fve6b/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3n0fve6b/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmps9a98o4t/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps9a98o4t/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvj65azq3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvj65azq3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1rlz6flv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1rlz6flv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpxtv1dzoa/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxtv1dzoa/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkii_dfwm/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkii_dfwm/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9adt5pgb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9adt5pgb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp31qal7ey/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp31qal7ey/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpb4cr4psi/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpb4cr4psi/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp82pvoyoo/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp82pvoyoo/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmmg1d4zb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmmg1d4zb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_338m_vu/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_338m_vu/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwyz7jtga/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwyz7jtga/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpm7vp5ax_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm7vp5ax_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppuwbu_nx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppuwbu_nx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpktkdppkq/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpktkdppkq/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_wt_tz8c/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_wt_tz8c/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpphukawub/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpphukawub/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpt3iqsp17/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpt3iqsp17/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_86ov1ys/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_86ov1ys/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7jud12sk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7jud12sk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9u27s47q/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9u27s47q/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5mw0mj2_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5mw0mj2_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvxd81t5f/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvxd81t5f/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpt_trqv5l/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpt_trqv5l/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmulwy_1n/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmulwy_1n/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp840i3fc2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp840i3fc2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3uoyljp1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3uoyljp1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpuzd7mk4w/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuzd7mk4w/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfa99e9x1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfa99e9x1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpe90cijhl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe90cijhl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_w44appg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_w44appg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpp5700dx8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp5700dx8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgjyf810m/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgjyf810m/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmph0cg6gv8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph0cg6gv8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4cyk3mtb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4cyk3mtb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptia_ryrp/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptia_ryrp/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqn3nezqv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqn3nezqv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp83pc8c6v/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp83pc8c6v/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmarj1aqm/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmarj1aqm/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6471tclz/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6471tclz/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp48mo9hg7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp48mo9hg7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpc4913xka/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpc4913xka/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpx1gpizo3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx1gpizo3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvbjpwpji/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvbjpwpji/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1_cxa242/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1_cxa242/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgmvssqiy/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgmvssqiy/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbft4cdhn/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbft4cdhn/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2bju24pe/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2bju24pe/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwkgmjzd5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwkgmjzd5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkhayo_tu/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkhayo_tu/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpa59q_q9p/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpa59q_q9p/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1onuf03_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1onuf03_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_i27446_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_i27446_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwglhwfhx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwglhwfhx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpclpdmu1y/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpclpdmu1y/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp178me7ii/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp178me7ii/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2krq10gm/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2krq10gm/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp92ly6a3b/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp92ly6a3b/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5c0629aa/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5c0629aa/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpj93zqxo2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpj93zqxo2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5jupmbw4/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5jupmbw4/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6_c0zqi5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6_c0zqi5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpk_jh_8wv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk_jh_8wv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6t_kthj5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6t_kthj5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpasudhrdr/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpasudhrdr/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpy1k_d0gl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpy1k_d0gl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpswznoejk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpswznoejk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6_2mgynd/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6_2mgynd/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp25jco0y2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp25jco0y2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjgxkwkti/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjgxkwkti/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8oz2ss58/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8oz2ss58/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1r6x3nfl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1r6x3nfl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmps63vrog1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps63vrog1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpuhas6_9e/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuhas6_9e/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_56d_73q/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_56d_73q/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfp1kaeqh/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfp1kaeqh/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5j0hfun6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5j0hfun6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpyuh9n3f3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyuh9n3f3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpavo74hxp/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpavo74hxp/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpxw4z1sf7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxw4z1sf7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4lwoipin/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4lwoipin/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8g3_a2w2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8g3_a2w2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkosuxqyn/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkosuxqyn/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmedq7kyj/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmedq7kyj/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpn31sjkc6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpn31sjkc6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpp3unrgta/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp3unrgta/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpp7v3spm1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp7v3spm1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpuuyhzwqt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuuyhzwqt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppbucd3yf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppbucd3yf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppwracx9h/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppwracx9h/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5qix63zq/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5qix63zq/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwo91bauf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwo91bauf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpuzmu3oao/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuzmu3oao/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgvqwayum/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgvqwayum/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpf20mbfbd/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpf20mbfbd/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmaajjt58/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmaajjt58/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmlz9ox2h/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmlz9ox2h/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpunv3g823/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpunv3g823/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpd92xni1c/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd92xni1c/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjwnk0e8i/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjwnk0e8i/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpuvt961c3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuvt961c3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpe4vlbs_l/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpe4vlbs_l/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppra1dd9y/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppra1dd9y/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpsp0x9dyk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsp0x9dyk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpluzq1tby/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpluzq1tby/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp62agpl1x/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp62agpl1x/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfhnvl6jg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfhnvl6jg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_tc47tnv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_tc47tnv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4y2mapbr/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4y2mapbr/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_y2m7vvx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_y2m7vvx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmb0ql8i5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmb0ql8i5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp31edmjx5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp31edmjx5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpemlvg1js/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpemlvg1js/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpb5tmba5u/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpb5tmba5u/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmprz7ihmlu/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprz7ihmlu/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5pl_qd3t/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5pl_qd3t/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0cebmifm/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0cebmifm/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2r6efwdh/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2r6efwdh/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnxgp4z5v/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnxgp4z5v/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpi069zfpw/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi069zfpw/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpldixiqc6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpldixiqc6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4b19zid0/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4b19zid0/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpo2qw2ar9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo2qw2ar9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6y7_b2kh/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6y7_b2kh/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzp4kprnn/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzp4kprnn/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdw45oqqz/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdw45oqqz/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpl5a3wx93/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpl5a3wx93/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptvq2jg69/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptvq2jg69/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdk0e9p8m/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdk0e9p8m/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpofsru95f/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpofsru95f/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpilv5svih/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpilv5svih/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpogzvf_jt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpogzvf_jt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpc70rg8we/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpc70rg8we/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpo486payg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo486payg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgzmw9xpn/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgzmw9xpn/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzloso4o4/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzloso4o4/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpps2g2e8s/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpps2g2e8s/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_rc1spnf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_rc1spnf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpx_iy4oky/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx_iy4oky/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpc07627h1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpc07627h1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjjkx365w/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjjkx365w/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgwlsuljz/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgwlsuljz/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpx8c96vx9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx8c96vx9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmprvgt6x4c/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprvgt6x4c/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfz22_l0m/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfz22_l0m/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbntdtbql/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbntdtbql/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmped34tnkj/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmped34tnkj/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpyv479rc6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyv479rc6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpers9ke_a/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpers9ke_a/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_iaut_pb/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_iaut_pb/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp41w95cs_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp41w95cs_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp40f5kz1p/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp40f5kz1p/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4m40snko/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4m40snko/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5ycl8_et/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5ycl8_et/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpd17kq3su/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd17kq3su/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpue26_gdo/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpue26_gdo/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5qz734u6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5qz734u6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphwbhy4u2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphwbhy4u2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpeoldoz1u/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpeoldoz1u/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpaciqexqm/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpaciqexqm/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmprmbw5zey/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprmbw5zey/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpxx716s53/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxx716s53/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzaaq526c/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzaaq526c/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkj119toe/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkj119toe/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpiukyaqom/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpiukyaqom/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgg3ttfqj/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgg3ttfqj/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6xq145cx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6xq145cx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmph7q0wg42/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph7q0wg42/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0fy51sg9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0fy51sg9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8g7hvrwc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8g7hvrwc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpygmpm4nf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpygmpm4nf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmphyqrb5h9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphyqrb5h9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0sfria1q/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0sfria1q/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp4395dxf7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4395dxf7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7yxq1smx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7yxq1smx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpebml27t_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpebml27t_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5_sxpo1x/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5_sxpo1x/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpyojwk7x7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyojwk7x7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbdpbl4lp/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbdpbl4lp/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpu35md825/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu35md825/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfkzuuany/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfkzuuany/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpd2jb1o23/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd2jb1o23/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvoaxh6f4/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvoaxh6f4/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpc86q4u1b/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpc86q4u1b/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8hn1fdpg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8hn1fdpg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3bp7di8e/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3bp7di8e/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0qbe8dh7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0qbe8dh7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplvdrsw8o/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplvdrsw8o/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpxj6dt_4h/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxj6dt_4h/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpj0eky24w/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpj0eky24w/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpx7sdixok/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpx7sdixok/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8r3zv_eg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8r3zv_eg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpxebqvn5a/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxebqvn5a/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbm9hldif/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbm9hldif/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpy3hgdvvv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpy3hgdvvv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5vxsgzrv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5vxsgzrv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpq4vqki2m/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpq4vqki2m/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp5i_9ntiv/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp5i_9ntiv/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpn6mu3pbg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpn6mu3pbg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppw_flbqe/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppw_flbqe/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpk7k6us4e/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk7k6us4e/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmprpe26gvf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprpe26gvf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdna58ure/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdna58ure/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgwym7snm/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgwym7snm/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0d3xbop6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0d3xbop6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpyoza0yaz/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyoza0yaz/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpw77zxpwq/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpw77zxpwq/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbcniseb4/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbcniseb4/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjkfpcb4s/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjkfpcb4s/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpm7bnd0_l/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm7bnd0_l/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmicx6xr7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmicx6xr7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpj3ccva2k/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpj3ccva2k/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpog42ppd5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpog42ppd5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmqrx0xy7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmqrx0xy7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpm8nc35k9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpm8nc35k9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpd7j8w_2m/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd7j8w_2m/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9416albt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9416albt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpyk68mvxw/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyk68mvxw/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkxpbdrek/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkxpbdrek/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptwzdoaig/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptwzdoaig/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpb1tfa79i/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpb1tfa79i/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8sz7w7ok/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8sz7w7ok/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzr6taemz/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzr6taemz/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpixnzby8n/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpixnzby8n/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpsugcl266/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpsugcl266/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpluy7vs4y/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpluy7vs4y/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7s8xzawc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7s8xzawc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpgo_1vxjw/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpgo_1vxjw/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1kacr9xi/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1kacr9xi/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8ay12ljs/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8ay12ljs/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_x6h9ncl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_x6h9ncl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0er8mnu5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0er8mnu5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpb6holrjp/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpb6holrjp/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbjuhkazx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbjuhkazx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3knt0cdg/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3knt0cdg/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpk1m37hwe/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk1m37hwe/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1zbwxel9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1zbwxel9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp6zksoogc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp6zksoogc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpo2wpvld3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo2wpvld3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpuieuqzak/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpuieuqzak/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpr9iczy0c/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpr9iczy0c/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp158ew547/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp158ew547/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpn6tzw0cf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpn6tzw0cf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjwj90d8k/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjwj90d8k/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpo7gzf1ub/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpo7gzf1ub/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkk92vm1r/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkk92vm1r/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_y9rcecd/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_y9rcecd/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwd0ripzc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwd0ripzc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmprn9f_ymt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprn9f_ymt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzrijlmfk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzrijlmfk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpkjbx54s6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpkjbx54s6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpauhctz62/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpauhctz62/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjmmf0i5m/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjmmf0i5m/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpa9fz0x4c/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpa9fz0x4c/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmprwx696bk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprwx696bk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8funs7qk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8funs7qk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8beb4tew/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8beb4tew/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpng99ff_d/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpng99ff_d/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp9re4y025/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9re4y025/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpcy5rh2k7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcy5rh2k7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp2ek8up96/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp2ek8up96/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpotd8renn/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpotd8renn/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7rjosed7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7rjosed7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptedr89f1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptedr89f1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmxkvj5sq/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmxkvj5sq/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbtgb23q_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbtgb23q_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqge22xr1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqge22xr1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp04cr9tzi/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp04cr9tzi/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpi3d17xuk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi3d17xuk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplr0csdes/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplr0csdes/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpww7noy0u/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpww7noy0u/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpy4p_brrx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpy4p_brrx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmprgox2rn_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmprgox2rn_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnpng9s30/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnpng9s30/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfi6pb0vt/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfi6pb0vt/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdm72er60/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdm72er60/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpzco031tl/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzco031tl/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpmjx7gxd4/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpmjx7gxd4/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0_0ajqo9/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0_0ajqo9/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpp7yowkql/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpp7yowkql/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpqipvsbj_/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpqipvsbj_/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpv7g0jdxs/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpv7g0jdxs/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmph7y_hj1a/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmph7y_hj1a/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1ippj4ma/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1ippj4ma/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpc2wld1ju/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpc2wld1ju/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp0a2tj2py/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp0a2tj2py/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7todioa3/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7todioa3/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpa32zuz2b/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpa32zuz2b/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1419qh_x/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1419qh_x/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpyf96bnr6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyf96bnr6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1arlzlbc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1arlzlbc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp15sbkwxq/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp15sbkwxq/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp_442qzz7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp_442qzz7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpl1e45vr7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpl1e45vr7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpk6mq4t3j/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpk6mq4t3j/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpyqo7vql1/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpyqo7vql1/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmps8m_5ehk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmps8m_5ehk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpjivyo3n8/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjivyo3n8/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp89t9ip9e/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp89t9ip9e/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpypbecw5h/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpypbecw5h/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvy_v_7lo/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvy_v_7lo/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdvzdk0n5/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdvzdk0n5/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpdnnggwdd/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdnnggwdd/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmppqabanbc/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppqabanbc/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvj3euv8g/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvj3euv8g/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpi2vx23iz/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi2vx23iz/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpvui0gbz6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpvui0gbz6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpu3s__24o/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpu3s__24o/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1i7ysnee/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1i7ysnee/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmplsbr8687/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmplsbr8687/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) ___________ test_three_in_a_row[strandedness_chain50-method_chain50] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same') method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 120 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain59-method_chain59] ___________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E /usr/lib/python3/dist-packages/pandas/core/common.py:143 E (and 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ___________________________ test_coverage[opposite] ____________________________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness = 'opposite' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", strandedness) tests/test_binary.py:207: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:238: in test_coverage result = gr.coverage(gr2, strandedness=strandedness) pyranges/pyranges.py:1341: in coverage other = other.merge(count=True, strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_coverage( E strandedness='opposite', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpb2wg4xml/f1.bed -b /tmp/tmpb2wg4xml/f2.bed Chromosome Start End Name Score Strand 0 chr1 9668963 9671079 a 0 + 1 chr1 2778250 2778661 a 0 + 2 chr1 1418927 1425121 a 0 + 3 chr1 1785204 1791237 a 0 + 4 chr1 6899199 6906990 a 0 + 5 chr1 4700813 4700914 a 0 + 6 chr1 9668963 9670971 a 0 - 7 chr3 3185279 3191312 a 0 - 8 chr10 1229967 1239189 a 0 - 9 chr22 10000000 10004071 a 0 + 10 chr22 5773160 5775060 a 0 + Chromosome Start End Name Score Strand 0 chr1 1326575 1326576 a 0 + 1 chr1 7502102 7505234 a 0 + 2 chr1 5601192 5602936 a 0 + 3 chr1 600806 603397 a 0 + 4 chr1 7682882 7682883 a 0 - 5 chr1 4252703 4253641 a 0 - 6 chr3 3013395 3017438 a 0 - 7 chr14 8743331 8752740 a 0 + 8 chr22 2573693 2581127 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpmnf80zh3/f1.bed -b /tmp/tmpmnf80zh3/f2.bed Chromosome Start End Name Score Strand 0 chr1 9668963 9671079 a 0 + 1 chr1 2778250 2778661 a 0 + 2 chr1 1418927 1425121 a 0 + 3 chr1 1785204 1791237 a 0 + 4 chr1 6899199 6906990 a 0 + 5 chr1 4700813 4700914 a 0 + 6 chr1 9668963 9670971 a 0 - 7 chr3 3185279 3191312 a 0 - 8 chr10 1229967 1230068 a 0 - 9 chr22 10000000 10004071 a 0 + 10 chr22 5773160 5775060 a 0 + Chromosome Start End Name Score Strand 0 chr1 1326575 1326576 a 0 + 1 chr1 7502102 7505234 a 0 + 2 chr1 5601192 5602936 a 0 + 3 chr1 600806 603397 a 0 + 4 chr1 7682882 7682883 a 0 - 5 chr1 4252703 4253641 a 0 - 6 chr3 3013395 3017438 a 0 - 7 chr14 8743331 8752740 a 0 + 8 chr22 2573693 2581127 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpjfetzzg_/f1.bed -b /tmp/tmpjfetzzg_/f2.bed Chromosome Start End Name Score Strand 0 chr1 9668963 9671079 a 0 + 1 chr1 2778250 2778661 a 0 + 2 chr1 1418927 1425121 a 0 + 3 chr1 1785204 1791237 a 0 + 4 chr1 6899199 6906990 a 0 + 5 chr1 4700813 4700914 a 0 + 6 chr1 9668963 9670971 a 0 - 7 chr3 3185279 3191312 a 0 - 8 chr10 1229967 1230068 a 0 - 9 chr22 10000000 10004071 a 0 + 10 chr22 5773160 5775060 a 0 + Chromosome Start End Name Score Strand 0 chr1 1326575 1326576 a 0 + 1 chr1 7502102 7502103 a 0 + 2 chr1 5601192 5602936 a 0 + 3 chr1 7682882 7682883 a 0 + 4 chr1 4252703 4252704 a 0 + 5 chr1 600806 600807 a 0 + 6 chr3 3013395 3017438 a 0 + 7 chr14 8743331 8743332 a 0 + 8 chr22 2573693 2573694 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0yyn_30q/f1.bed -b /tmp/tmp0yyn_30q/f2.bed Chromosome Start End Name Score Strand 0 chr1 9668963 9671079 a 0 + 1 chr1 2778250 2778661 a 0 + 2 chr1 1418927 1425121 a 0 + 3 chr1 1785204 1791237 a 0 + 4 chr1 6899199 6906990 a 0 + 5 chr1 4700813 4700914 a 0 + 6 chr1 9668963 9670971 a 0 - 7 chr3 3185279 3191312 a 0 - 8 chr10 1229967 1230068 a 0 - 9 chr22 10000000 10004071 a 0 + 10 chr22 5773160 5773161 a 0 + Chromosome Start End Name Score Strand 0 chr1 1326575 1326576 a 0 + 1 chr1 7502102 7502103 a 0 + 2 chr1 5601192 5602936 a 0 + 3 chr1 7682882 7682883 a 0 + 4 chr1 4252703 4252704 a 0 + 5 chr1 600806 600807 a 0 + 6 chr3 3013395 3017438 a 0 + 7 chr14 8743331 8743332 a 0 + 8 chr22 2573693 2573694 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6pw0ni9j/f1.bed -b /tmp/tmp6pw0ni9j/f2.bed Chromosome Start End Name Score Strand 0 chr1 9668963 9671079 a 0 + 1 chr1 2778250 2778661 a 0 + 2 chr1 1418927 1425121 a 0 + 3 chr1 1785204 1791237 a 0 + 4 chr1 6899199 6906990 a 0 + 5 chr1 4700813 4700914 a 0 + 6 chr1 9668963 9670971 a 0 - 7 chr3 3185279 3191312 a 0 - 8 chr10 1229967 1230068 a 0 - 9 chr22 10000000 10004071 a 0 + 10 chr22 5773160 5773161 a 0 + Chromosome Start End Name Score Strand 0 chr9 2 3 a 0 - 1 chr9 2 3 a 0 - 2 chr9 2 3 a 0 - 3 chr9 2 3 a 0 - 4 chr9 2 3 a 0 - 5 chr9 2 3 a 0 - 6 chr9 2 3 a 0 - 7 chr9 2 3 a 0 - 8 chr9 2 3 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpwei96p49/f1.bed -b /tmp/tmpwei96p49/f2.bed Chromosome Start End Name Score Strand 0 chr1 9668963 9671079 a 0 + 1 chr1 2778250 2778661 a 0 + 2 chr1 1418927 1425121 a 0 + 3 chr1 1785204 1791237 a 0 + 4 chr1 6899199 6906990 a 0 + 5 chr1 4700813 4700914 a 0 + 6 chr1 9668963 9670971 a 0 - 7 chr3 3185279 3191312 a 0 - 8 chr10 1229967 1230068 a 0 - 9 chr22 10000000 10004071 a 0 + 10 chr22 5773160 5773161 a 0 + Chromosome Start End Name Score Strand 0 chr1 9668963 9671079 a 0 + 1 chr1 2778250 2778661 a 0 + 2 chr1 1418927 1425121 a 0 + 3 chr1 1785204 1791237 a 0 + 4 chr1 6899199 6906990 a 0 + 5 chr1 4700813 4700914 a 0 + 6 chr1 9668963 9670971 a 0 - 7 chr3 3185279 3191312 a 0 - 8 chr10 1229967 1230068 a 0 - 9 chr22 10000000 10004071 a 0 + 10 chr22 5773160 5773161 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpmjdxdo7m/f1.bed -b /tmp/tmpmjdxdo7m/f2.bed Chromosome Start End Name Score Strand 0 chr1 9668963 9671079 a 0 + 1 chr1 2778250 2778661 a 0 + 2 chr1 1418927 1425121 a 0 + 3 chr1 1785204 1791237 a 0 + 4 chr1 4700813 4700914 a 0 + 5 chr1 9668963 9670971 a 0 - 6 chr3 6899199 6906990 a 0 + 7 chr3 3185279 3191312 a 0 - 8 chr10 1229967 1230068 a 0 - 9 chr22 10000000 10004071 a 0 + 10 chr22 5773160 5773161 a 0 + Chromosome Start End Name Score Strand 0 chr1 9668963 9671079 a 0 + 1 chr1 2778250 2778661 a 0 + 2 chr1 1418927 1425121 a 0 + 3 chr1 1785204 1791237 a 0 + 4 chr1 6899199 6906990 a 0 + 5 chr1 4700813 4700914 a 0 + 6 chr1 9668963 9670971 a 0 - 7 chr3 3185279 3191312 a 0 - 8 chr10 1229967 1230068 a 0 - 9 chr22 10000000 10004071 a 0 + 10 chr22 5773160 5773161 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmprdbapybq/f1.bed -b /tmp/tmprdbapybq/f2.bed Chromosome Start End Name Score Strand 0 chr1 614432 621047 a 0 - 1 chr2 4050614 4053570 a 0 + 2 chr2 7736295 7744171 a 0 - 3 chr13 7304591 7311663 a 0 + 4 chr14 8102510 8105254 a 0 + 5 chr19 8833244 8840870 a 0 + Chromosome Start End Name Score Strand 0 chr1 5143190 5145274 a 0 + 1 chr1 7805840 7807934 a 0 + 2 chr1 3667178 3670503 a 0 + 3 chr1 3372379 3375184 a 0 + 4 chr4 1 6170 a 0 + 5 chr7 5428435 5436343 a 0 + 6 chr13 844775 853544 a 0 - 7 chr16 1948818 1952004 a 0 + 8 chr19 1901494 1911493 a 0 + 9 chr20 2659858 2665403 a 0 + 10 chr22 2479154 2489154 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppm1jj66b/f1.bed -b /tmp/tmppm1jj66b/f2.bed Chromosome Start End Name Score Strand 0 chr1 614432 621047 a 0 - 1 chr2 4050614 4053570 a 0 + 2 chr2 7736295 7744171 a 0 - 3 chr13 7304591 7311663 a 0 + 4 chr14 8102510 8105254 a 0 + 5 chr19 8833244 8840870 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + 1 chr1 1 2 a 0 + 2 chr1 1 2 a 0 + 3 chr1 1 2 a 0 + 4 chr1 1 2 a 0 + 5 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpz1z0u_lm/f1.bed -b /tmp/tmpz1z0u_lm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpa13u15m5/f1.bed -b /tmp/tmpa13u15m5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqbtasunh/f1.bed -b /tmp/tmpqbtasunh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpr5v2qua0/f1.bed -b /tmp/tmpr5v2qua0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5fdyq_pk/f1.bed -b /tmp/tmp5fdyq_pk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 10000000 10006256 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpfnuy8axt/f1.bed -b /tmp/tmpfnuy8axt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpa8oc2zsz/f1.bed -b /tmp/tmpa8oc2zsz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5692188 5699124 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpftlbhxkh/f1.bed -b /tmp/tmpftlbhxkh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5ckpxuix/f1.bed -b /tmp/tmp5ckpxuix/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9999999 10004013 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdfxm3f6i/f1.bed -b /tmp/tmpdfxm3f6i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxo0qgmkt/f1.bed -b /tmp/tmpxo0qgmkt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8400795 8408736 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpbe9pjhfg/f1.bed -b /tmp/tmpbe9pjhfg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2n_we07r/f1.bed -b /tmp/tmp2n_we07r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1462825 1470645 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpmor8d6yg/f1.bed -b /tmp/tmpmor8d6yg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpf4kns3bv/f1.bed -b /tmp/tmpf4kns3bv/f2.bed Chromosome Start End Name Score Strand 0 chr1 3099 3100 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9963 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmposgtsl4z/f1.bed -b /tmp/tmposgtsl4z/f2.bed Chromosome Start End Name Score Strand 0 chr1 3099 3100 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpux9ljem0/f1.bed -b /tmp/tmpux9ljem0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4415806 4421453 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpip29c8xh/f1.bed -b /tmp/tmpip29c8xh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpi4vr3yvq/f1.bed -b /tmp/tmpi4vr3yvq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr10 1 9754 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2nqsk517/f1.bed -b /tmp/tmp2nqsk517/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpm01i36u4/f1.bed -b /tmp/tmpm01i36u4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9437151 9444764 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpwtq89r8q/f1.bed -b /tmp/tmpwtq89r8q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_ld5or4i/f1.bed -b /tmp/tmp_ld5or4i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3021624 3027701 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpa6q6qxjt/f1.bed -b /tmp/tmpa6q6qxjt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6zio0ul0/f1.bed -b /tmp/tmp6zio0ul0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4521048 4523952 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpj6wjnbqv/f1.bed -b /tmp/tmpj6wjnbqv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmprgrosk66/f1.bed -b /tmp/tmprgrosk66/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 68343 70558 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpewwsurgu/f1.bed -b /tmp/tmpewwsurgu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpjgdo1ien/f1.bed -b /tmp/tmpjgdo1ien/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9565498 9574170 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp801uib0h/f1.bed -b /tmp/tmp801uib0h/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0s330ams/f1.bed -b /tmp/tmp0s330ams/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5953971 5957584 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpbd1k8xu2/f1.bed -b /tmp/tmpbd1k8xu2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpm2rzjtvw/f1.bed -b /tmp/tmpm2rzjtvw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 218256 218844 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpijods5bp/f1.bed -b /tmp/tmpijods5bp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppp7zxyb7/f1.bed -b /tmp/tmppp7zxyb7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7595742 7599006 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpe019h_85/f1.bed -b /tmp/tmpe019h_85/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqbquaebz/f1.bed -b /tmp/tmpqbquaebz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 3969 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1ljxhzyk/f1.bed -b /tmp/tmp1ljxhzyk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8g43t2a4/f1.bed -b /tmp/tmp8g43t2a4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5576782 5581876 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpso_4rhts/f1.bed -b /tmp/tmpso_4rhts/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpj1klf_ln/f1.bed -b /tmp/tmpj1klf_ln/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1598042 1602287 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp025d9tj9/f1.bed -b /tmp/tmp025d9tj9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgbnxi3u0/f1.bed -b /tmp/tmpgbnxi3u0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9806865 9808311 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpugmokmc6/f1.bed -b /tmp/tmpugmokmc6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmps49k8mst/f1.bed -b /tmp/tmps49k8mst/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2 2002 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpirnas3t_/f1.bed -b /tmp/tmpirnas3t_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7r3apojd/f1.bed -b /tmp/tmp7r3apojd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2977 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqdt0rmrn/f1.bed -b /tmp/tmpqdt0rmrn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpscvkag2q/f1.bed -b /tmp/tmpscvkag2q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7315105 7317787 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpuyyigggj/f1.bed -b /tmp/tmpuyyigggj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp01slkmz4/f1.bed -b /tmp/tmp01slkmz4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8791580 8799852 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpz_jattol/f1.bed -b /tmp/tmpz_jattol/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpml9qwvfk/f1.bed -b /tmp/tmpml9qwvfk/f2.bed Chromosome Start End Name Score Strand 0 chr1 5350 5351 a 0 - 1 chr1 5350 5351 a 0 - Chromosome Start End Name Score Strand 0 chr1 8786090 8790202 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpit2vmj3d/f1.bed -b /tmp/tmpit2vmj3d/f2.bed Chromosome Start End Name Score Strand 0 chr1 5350 5351 a 0 - 1 chr1 5350 5351 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdw7ao6qx/f1.bed -b /tmp/tmpdw7ao6qx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1497678 1507678 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2xln2r39/f1.bed -b /tmp/tmp2xln2r39/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6264213 6268469 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxb7peyk8/f1.bed -b /tmp/tmpxb7peyk8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpcwgda4v2/f1.bed -b /tmp/tmpcwgda4v2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9416250 9422712 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpofoyzou0/f1.bed -b /tmp/tmpofoyzou0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgp8qs5ya/f1.bed -b /tmp/tmpgp8qs5ya/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9663485 9667636 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpmqmqdlal/f1.bed -b /tmp/tmpmqmqdlal/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpmffswl5y/f1.bed -b /tmp/tmpmffswl5y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8944282 8947613 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpjyqo5jlr/f1.bed -b /tmp/tmpjyqo5jlr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmprkd4ls0s/f1.bed -b /tmp/tmprkd4ls0s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9748296 9748540 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpumwcwtwo/f1.bed -b /tmp/tmpumwcwtwo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp77j6r9ql/f1.bed -b /tmp/tmp77j6r9ql/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4398437 4400042 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8awqqf9n/f1.bed -b /tmp/tmp8awqqf9n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpbfg39o4_/f1.bed -b /tmp/tmpbfg39o4_/f2.bed Chromosome Start End Name Score Strand 0 chr1 4327 4328 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 8984 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5_gtbidy/f1.bed -b /tmp/tmp5_gtbidy/f2.bed Chromosome Start End Name Score Strand 0 chr1 4327 4328 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpguwt6o9d/f1.bed -b /tmp/tmpguwt6o9d/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6703797 6712696 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpf8opzpt5/f1.bed -b /tmp/tmpf8opzpt5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp03tfnf5g/f1.bed -b /tmp/tmp03tfnf5g/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1099735 1105796 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpiefvvybk/f1.bed -b /tmp/tmpiefvvybk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpsa3j3i1j/f1.bed -b /tmp/tmpsa3j3i1j/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7807273 7809914 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpvdk0hj4w/f1.bed -b /tmp/tmpvdk0hj4w/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpk3zdu46x/f1.bed -b /tmp/tmpk3zdu46x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9195865 9204386 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppmxead8g/f1.bed -b /tmp/tmppmxead8g/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1gi3h37_/f1.bed -b /tmp/tmp1gi3h37_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 557311 557312 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp3s5b87bp/f1.bed -b /tmp/tmp3s5b87bp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp840_oadi/f1.bed -b /tmp/tmp840_oadi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9587435 9590564 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpfl8ttlp4/f1.bed -b /tmp/tmpfl8ttlp4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpkep4ey_e/f1.bed -b /tmp/tmpkep4ey_e/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4202130 4208998 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgx1r6pct/f1.bed -b /tmp/tmpgx1r6pct/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4u8d__3v/f1.bed -b /tmp/tmp4u8d__3v/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7389975 7391611 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpiswpbt5n/f1.bed -b /tmp/tmpiswpbt5n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpeauqo9pc/f1.bed -b /tmp/tmpeauqo9pc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6230964 6233125 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp28prbush/f1.bed -b /tmp/tmp28prbush/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpoanxw15c/f1.bed -b /tmp/tmpoanxw15c/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9518636 9528636 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpwelzakk9/f1.bed -b /tmp/tmpwelzakk9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpoettheoo/f1.bed -b /tmp/tmpoettheoo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2270779 2274578 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpjmog4e26/f1.bed -b /tmp/tmpjmog4e26/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpsyl9_emf/f1.bed -b /tmp/tmpsyl9_emf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4681221 4690910 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpaqamzo2y/f1.bed -b /tmp/tmpaqamzo2y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzsrt29rm/f1.bed -b /tmp/tmpzsrt29rm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6165934 6169995 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpaphe7oo1/f1.bed -b /tmp/tmpaphe7oo1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2157873 2159842 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp3mugozp9/f1.bed -b /tmp/tmp3mugozp9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp3tt9o_mz/f1.bed -b /tmp/tmp3tt9o_mz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6901809 6902744 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpe_bxr0xm/f1.bed -b /tmp/tmpe_bxr0xm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0mtytwqn/f1.bed -b /tmp/tmp0mtytwqn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8071557 8075663 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8asqxjos/f1.bed -b /tmp/tmp8asqxjos/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpbp0sttvs/f1.bed -b /tmp/tmpbp0sttvs/f2.bed Chromosome Start End Name Score Strand 0 chr1 3594 3595 a 0 - 1 chr1 3594 3595 a 0 - Chromosome Start End Name Score Strand 0 chr1 380474 386181 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0pbt4m_n/f1.bed -b /tmp/tmp0pbt4m_n/f2.bed Chromosome Start End Name Score Strand 0 chr1 3594 3595 a 0 - 1 chr1 3594 3595 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpi0bgj4nr/f1.bed -b /tmp/tmpi0bgj4nr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8378031 8380556 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpkoo3ccos/f1.bed -b /tmp/tmpkoo3ccos/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_01pyhte/f1.bed -b /tmp/tmp_01pyhte/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7348272 7348499 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9vfhpg0r/f1.bed -b /tmp/tmp9vfhpg0r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpg1gv_v5k/f1.bed -b /tmp/tmpg1gv_v5k/f2.bed Chromosome Start End Name Score Strand 0 chr1 5005 5006 a 0 - 1 chr1 5005 5006 a 0 - Chromosome Start End Name Score Strand 0 chr1 634249 636149 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpw1ahovg1/f1.bed -b /tmp/tmpw1ahovg1/f2.bed Chromosome Start End Name Score Strand 0 chr1 5005 5006 a 0 - 1 chr1 5005 5006 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpd7n1qbac/f1.bed -b /tmp/tmpd7n1qbac/f2.bed Chromosome Start End Name Score Strand 0 chr1 2185 2186 a 0 - 1 chr1 2185 2186 a 0 - Chromosome Start End Name Score Strand 0 chr1 1630243 1639166 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpsndwos76/f1.bed -b /tmp/tmpsndwos76/f2.bed Chromosome Start End Name Score Strand 0 chr1 2185 2186 a 0 - 1 chr1 2185 2186 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzv7yuj8y/f1.bed -b /tmp/tmpzv7yuj8y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5320356 5320426 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmptjacfkvm/f1.bed -b /tmp/tmptjacfkvm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpk5lzke7v/f1.bed -b /tmp/tmpk5lzke7v/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2399214 2404099 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqydk_3u1/f1.bed -b /tmp/tmpqydk_3u1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpcurveb8f/f1.bed -b /tmp/tmpcurveb8f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9999999 10005696 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpml_50u8v/f1.bed -b /tmp/tmpml_50u8v/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpkzyz_177/f1.bed -b /tmp/tmpkzyz_177/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5264504 5269784 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_fe4cuhd/f1.bed -b /tmp/tmp_fe4cuhd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1m7cde0d/f1.bed -b /tmp/tmp1m7cde0d/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4978204 4981877 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpc9tmd2nu/f1.bed -b /tmp/tmpc9tmd2nu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzheg4owo/f1.bed -b /tmp/tmpzheg4owo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6722585 6727976 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpjfblfak5/f1.bed -b /tmp/tmpjfblfak5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7fk6taxe/f1.bed -b /tmp/tmp7fk6taxe/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6300915 6308100 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpsjviewld/f1.bed -b /tmp/tmpsjviewld/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmphzp8xrvj/f1.bed -b /tmp/tmphzp8xrvj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6859250 6861027 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpt2oph4fd/f1.bed -b /tmp/tmpt2oph4fd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpngtk9i1d/f1.bed -b /tmp/tmpngtk9i1d/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5660425 5669532 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpcub14cbu/f1.bed -b /tmp/tmpcub14cbu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4b6zkoc5/f1.bed -b /tmp/tmp4b6zkoc5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2403 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpmer0shsg/f1.bed -b /tmp/tmpmer0shsg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8y97la6n/f1.bed -b /tmp/tmp8y97la6n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4599823 4602155 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_vzvqwxp/f1.bed -b /tmp/tmp_vzvqwxp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxwek0n7p/f1.bed -b /tmp/tmpxwek0n7p/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 7886 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpwr84q18s/f1.bed -b /tmp/tmpwr84q18s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppjtop509/f1.bed -b /tmp/tmppjtop509/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr6 2774183 2779090 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1tyvqzce/f1.bed -b /tmp/tmp1tyvqzce/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpb2wxmflp/f1.bed -b /tmp/tmpb2wxmflp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3633779 3642363 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpb72m065n/f1.bed -b /tmp/tmpb72m065n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpbrmospsd/f1.bed -b /tmp/tmpbrmospsd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8347245 8353768 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpcgbigg48/f1.bed -b /tmp/tmpcgbigg48/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpaoaip5g7/f1.bed -b /tmp/tmpaoaip5g7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2327372 2336416 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpcg8dbopk/f1.bed -b /tmp/tmpcg8dbopk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpr5cqhngp/f1.bed -b /tmp/tmpr5cqhngp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5236127 5236128 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5pvmdg10/f1.bed -b /tmp/tmp5pvmdg10/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpv9v47f3m/f1.bed -b /tmp/tmpv9v47f3m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8518863 8524312 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpm6unr9oi/f1.bed -b /tmp/tmpm6unr9oi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmphk9xf6j3/f1.bed -b /tmp/tmphk9xf6j3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9999999 10009999 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpa7zsyglc/f1.bed -b /tmp/tmpa7zsyglc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpezkyr3d_/f1.bed -b /tmp/tmpezkyr3d_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 195582 201453 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpwek6c63a/f1.bed -b /tmp/tmpwek6c63a/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9jqbku5y/f1.bed -b /tmp/tmp9jqbku5y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1192386 1200161 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgd18u0bq/f1.bed -b /tmp/tmpgd18u0bq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1chzs2pp/f1.bed -b /tmp/tmp1chzs2pp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5270035 5275375 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxdktkw1e/f1.bed -b /tmp/tmpxdktkw1e/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpn18dqhzu/f1.bed -b /tmp/tmpn18dqhzu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5691505 5697068 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_yfpr87a/f1.bed -b /tmp/tmp_yfpr87a/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpq94m2luj/f1.bed -b /tmp/tmpq94m2luj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3427418 3433402 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp3lmksc7m/f1.bed -b /tmp/tmp3lmksc7m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4hkiovo7/f1.bed -b /tmp/tmp4hkiovo7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 782149 787116 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpv5c1x4yo/f1.bed -b /tmp/tmpv5c1x4yo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4oxclsx0/f1.bed -b /tmp/tmp4oxclsx0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9146573 9155054 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp92zearqg/f1.bed -b /tmp/tmp92zearqg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpfysj9gkk/f1.bed -b /tmp/tmpfysj9gkk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6545442 6547806 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzw4ax3_j/f1.bed -b /tmp/tmpzw4ax3_j/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpalyluocq/f1.bed -b /tmp/tmpalyluocq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5910921 5916581 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpvbga8nix/f1.bed -b /tmp/tmpvbga8nix/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp3i4kuao5/f1.bed -b /tmp/tmp3i4kuao5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr14 5794167 5800840 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpiepqqvwy/f1.bed -b /tmp/tmpiepqqvwy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5weeotes/f1.bed -b /tmp/tmp5weeotes/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8217274 8225434 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5o6mc50m/f1.bed -b /tmp/tmp5o6mc50m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpnco8slzb/f1.bed -b /tmp/tmpnco8slzb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3896814 3899961 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2gxf8av1/f1.bed -b /tmp/tmp2gxf8av1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpn0xue5l9/f1.bed -b /tmp/tmpn0xue5l9/f2.bed Chromosome Start End Name Score Strand 0 chr1 4038 4039 a 0 - 1 chr1 4038 4039 a 0 - Chromosome Start End Name Score Strand 0 chr1 2277929 2279800 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp23r7vom8/f1.bed -b /tmp/tmp23r7vom8/f2.bed Chromosome Start End Name Score Strand 0 chr1 4038 4039 a 0 - 1 chr1 4038 4039 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_je3i6bq/f1.bed -b /tmp/tmp_je3i6bq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp14ihq3fy/f1.bed -b /tmp/tmp14ihq3fy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppok0vpo1/f1.bed -b /tmp/tmppok0vpo1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2804321 2809861 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpq8glei_3/f1.bed -b /tmp/tmpq8glei_3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpvbjxr14y/f1.bed -b /tmp/tmpvbjxr14y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5709636 5719566 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpryngytel/f1.bed -b /tmp/tmpryngytel/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdf13gjn0/f1.bed -b /tmp/tmpdf13gjn0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4113264 4113605 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpo7tohbsj/f1.bed -b /tmp/tmpo7tohbsj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqzw9a7co/f1.bed -b /tmp/tmpqzw9a7co/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6988728 6989304 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpajt055xj/f1.bed -b /tmp/tmpajt055xj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmptset8kdi/f1.bed -b /tmp/tmptset8kdi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6690193 6696696 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpq23nxe3x/f1.bed -b /tmp/tmpq23nxe3x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3698299 3708188 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmplc9vdisg/f1.bed -b /tmp/tmplc9vdisg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxoglolol/f1.bed -b /tmp/tmpxoglolol/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 - 1 chr2 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 602077 611757 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6p3_9q_5/f1.bed -b /tmp/tmp6p3_9q_5/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 - 1 chr2 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppegi_w31/f1.bed -b /tmp/tmppegi_w31/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3151234 3157951 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp74aei08s/f1.bed -b /tmp/tmp74aei08s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpo2lb_dw3/f1.bed -b /tmp/tmpo2lb_dw3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3213703 3222835 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpvnxx55ga/f1.bed -b /tmp/tmpvnxx55ga/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0e8rs6nv/f1.bed -b /tmp/tmp0e8rs6nv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4993456 4995992 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxvhr64qv/f1.bed -b /tmp/tmpxvhr64qv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0cgvyyhw/f1.bed -b /tmp/tmp0cgvyyhw/f2.bed Chromosome Start End Name Score Strand 0 chr1 3109 3110 a 0 - 1 chr1 3109 3110 a 0 - Chromosome Start End Name Score Strand 0 chr1 3256 9752 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpp9_6k26h/f1.bed -b /tmp/tmpp9_6k26h/f2.bed Chromosome Start End Name Score Strand 0 chr1 3109 3110 a 0 - 1 chr1 3109 3110 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmplrkfh4bo/f1.bed -b /tmp/tmplrkfh4bo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 104555 106490 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzj8vnupm/f1.bed -b /tmp/tmpzj8vnupm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpmsg8xuyi/f1.bed -b /tmp/tmpmsg8xuyi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9972198 9977685 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp8f90xcut/f1.bed -b /tmp/tmp8f90xcut/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpu1jtahh2/f1.bed -b /tmp/tmpu1jtahh2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 3684 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpt6f_e5p6/f1.bed -b /tmp/tmpt6f_e5p6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 3323 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpk8yhgemd/f1.bed -b /tmp/tmpk8yhgemd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6702308 6705745 a 0 + 1 chr14 7277458 7279103 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpyamqqm8m/f1.bed -b /tmp/tmpyamqqm8m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9999999 10003088 a 0 - 1 chrX 9360572 9370012 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpaaa6cukq/f1.bed -b /tmp/tmpaaa6cukq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4665345 4666422 a 0 - 1 chr7 3209016 3210632 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgi55x7qk/f1.bed -b /tmp/tmpgi55x7qk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4468876 4473147 a 0 - 1 chr22 6698915 6705070 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpiqwxigul/f1.bed -b /tmp/tmpiqwxigul/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7059099 7066982 a 0 + 1 chr18 5837577 5845460 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4am0foyw/f1.bed -b /tmp/tmp4am0foyw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5445013 5445658 a 0 + 1 chr1 3958267 3962338 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpcs6r6p15/f1.bed -b /tmp/tmpcs6r6p15/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1758053 1765967 a 0 - 1 chr8 641837 642482 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpha7mp93y/f1.bed -b /tmp/tmpha7mp93y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 10000000 10005808 a 0 - 1 chr1 3314057 3315022 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpll2_8f_n/f1.bed -b /tmp/tmpll2_8f_n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9214844 9222906 a 0 - 1 chr1 759661 766345 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpnct8ndgb/f1.bed -b /tmp/tmpnct8ndgb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2004232 2013039 a 0 - 1 chr1 4525787 4527956 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1szm_oe8/f1.bed -b /tmp/tmp1szm_oe8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7198718 7205104 a 0 - 1 chr3 6485550 6492800 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpnhzc33m5/f1.bed -b /tmp/tmpnhzc33m5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8211881 8218351 a 0 - 1 chrX 2856323 2862793 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1mmqul2o/f1.bed -b /tmp/tmp1mmqul2o/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3271528 3272835 a 0 - 1 chr4 8792751 8796420 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7dw9z3e4/f1.bed -b /tmp/tmp7dw9z3e4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2561255 2568940 a 0 + 1 chr1 2561255 2566455 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpi8qrfxu4/f1.bed -b /tmp/tmpi8qrfxu4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6768863 6777175 a 0 + 1 chr1 188149 197267 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpg3xlx9v8/f1.bed -b /tmp/tmpg3xlx9v8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1787794 1791160 a 0 - 1 chr22 7922615 7927015 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4cr5mq0o/f1.bed -b /tmp/tmp4cr5mq0o/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 575550 575638 a 0 - 1 chr17 4329298 4334731 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpfgp3pw4_/f1.bed -b /tmp/tmpfgp3pw4_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9999999 10002051 a 0 - 1 chr7 361154 370522 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpvwe3q4b7/f1.bed -b /tmp/tmpvwe3q4b7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4621341 4624937 a 0 + 1 chr1 6439065 6441610 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_zfuq3dy/f1.bed -b /tmp/tmp_zfuq3dy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3916961 3923306 a 0 + 1 chr7 7318402 7327654 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5maw63vo/f1.bed -b /tmp/tmp5maw63vo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 547491 550186 a 0 + 1 chr1 4846495 4847584 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpk951sxpj/f1.bed -b /tmp/tmpk951sxpj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 270926 271573 a 0 - 1 chr1 7534619 7544593 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgw1_qbe0/f1.bed -b /tmp/tmpgw1_qbe0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4396658 4403008 a 0 - 1 chr20 2963431 2972404 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_6j0h6zu/f1.bed -b /tmp/tmp_6j0h6zu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 5911 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpe6jczi_e/f1.bed -b /tmp/tmpe6jczi_e/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 1677 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpm5pfx3m8/f1.bed -b /tmp/tmpm5pfx3m8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8325004 8329580 a 0 - 1 chr18 7405799 7409603 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpsol_0r1r/f1.bed -b /tmp/tmpsol_0r1r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 411261 411547 a 0 + 1 chr1 140559 140845 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpp1a9z6g2/f1.bed -b /tmp/tmpp1a9z6g2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 5025 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqjk6w_jj/f1.bed -b /tmp/tmpqjk6w_jj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5662885 5666308 a 0 - 1 chr9 8855141 8862016 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2xqll7pl/f1.bed -b /tmp/tmp2xqll7pl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 416375 424434 a 0 - 1 chr1 8867098 8870107 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpavjwk81t/f1.bed -b /tmp/tmpavjwk81t/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9454921 9457343 a 0 - 1 chrX 1183951 1192408 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpjf810040/f1.bed -b /tmp/tmpjf810040/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 8162 a 0 + 1 chr1 1 8162 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1fbdg9jh/f1.bed -b /tmp/tmp1fbdg9jh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7677437 7683382 a 0 - 1 chr4 2544544 2549275 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpth3ikbgl/f1.bed -b /tmp/tmpth3ikbgl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1408260 1409181 a 0 - 1 chr16 8294190 8304190 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1jcf2udy/f1.bed -b /tmp/tmp1jcf2udy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpx1nu7vsh/f1.bed -b /tmp/tmpx1nu7vsh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5214340 5214721 a 0 + 1 chr1 9044347 9044833 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpftkl3gss/f1.bed -b /tmp/tmpftkl3gss/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 8663 a 0 + 1 chr1 1 8663 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmplfc3n1ki/f1.bed -b /tmp/tmplfc3n1ki/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 10000 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpmrdlz93x/f1.bed -b /tmp/tmpmrdlz93x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 211846 220510 a 0 + 1 chr1 1 3967 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpu6gozcrv/f1.bed -b /tmp/tmpu6gozcrv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8987922 8992401 a 0 + 1 chr7 5069721 5074009 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7s3wtifa/f1.bed -b /tmp/tmp7s3wtifa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 3871 a 0 + 1 chr1 1 3871 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpv82xlfy3/f1.bed -b /tmp/tmpv82xlfy3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4721057 4727886 a 0 - 1 chr5 4721057 4721924 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpz81su0kg/f1.bed -b /tmp/tmpz81su0kg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9149995 9156611 a 0 + 1 chr1 6496924 6503874 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpmqbt67oe/f1.bed -b /tmp/tmpmqbt67oe/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 370 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_o5s99q1/f1.bed -b /tmp/tmp_o5s99q1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4742165 4744548 a 0 - 1 chr9 7002909 7004952 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp3trzzm88/f1.bed -b /tmp/tmp3trzzm88/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8755679 8762071 a 0 - 1 chr1 5901810 5911299 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzck4_fp8/f1.bed -b /tmp/tmpzck4_fp8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7723934 7733188 a 0 + 1 chr5 3925039 3929860 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpq4xtn_pg/f1.bed -b /tmp/tmpq4xtn_pg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2920573 2929577 a 0 - 1 chr1 1 9402 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6__r6atm/f1.bed -b /tmp/tmp6__r6atm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6361394 6363991 a 0 - 1 chrX 3053076 3057181 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpq3p_qxs6/f1.bed -b /tmp/tmpq3p_qxs6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6787046 6792791 a 0 + 1 chr13 3422415 3431452 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpyrfeum0f/f1.bed -b /tmp/tmpyrfeum0f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8268630 8275159 a 0 + 1 chr2 4632220 4632864 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpwsrvt0q_/f1.bed -b /tmp/tmpwsrvt0q_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1296301 1301851 a 0 - 1 chr21 7039672 7047441 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmprbbxsqqi/f1.bed -b /tmp/tmprbbxsqqi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4863257 4865195 a 0 - 1 chr5 7179986 7188998 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmprpcyeq3p/f1.bed -b /tmp/tmprpcyeq3p/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr4 6556968 6560472 a 0 - 1 chr9 949853 957777 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9obkbe7r/f1.bed -b /tmp/tmp9obkbe7r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3552618 3561849 a 0 + 1 chr15 2 2822 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpuj0slf58/f1.bed -b /tmp/tmpuj0slf58/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 833 a 0 - 1 chr1 1 833 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1qg5rp4n/f1.bed -b /tmp/tmp1qg5rp4n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 969309 975103 a 0 + 1 chr3 3348179 3348324 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6eyrvb6y/f1.bed -b /tmp/tmp6eyrvb6y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9252 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmplcv5mth7/f1.bed -b /tmp/tmplcv5mth7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9633151 9634093 a 0 + 1 chr1 15972 22966 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4lhmi8i7/f1.bed -b /tmp/tmp4lhmi8i7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9456074 9460229 a 0 + 1 chr1 9945190 9952845 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4115ffah/f1.bed -b /tmp/tmp4115ffah/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 266020 268736 a 0 + 1 chr1 2719880 2728435 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdpe8ob1z/f1.bed -b /tmp/tmpdpe8ob1z/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 679231 679310 a 0 + 1 chr1 1131925 1135855 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_94khtz4/f1.bed -b /tmp/tmp_94khtz4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2969557 2977557 a 0 + 1 chr1 7739246 7741785 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpovaaeh0b/f1.bed -b /tmp/tmpovaaeh0b/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 4200 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmptid1xllq/f1.bed -b /tmp/tmptid1xllq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5829601 5838625 a 0 + 1 chr10 8650276 8656527 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5idb9wfq/f1.bed -b /tmp/tmp5idb9wfq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 6319 a 0 - 1 chr1 1 6319 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgdwguny0/f1.bed -b /tmp/tmpgdwguny0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9999999 10009043 a 0 + 1 chr12 7330742 7335798 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmps8wpj7g6/f1.bed -b /tmp/tmps8wpj7g6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4713195 4720910 a 0 + 1 chr1 1275789 1279476 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_cd3hxqu/f1.bed -b /tmp/tmp_cd3hxqu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1110118 1117083 a 0 + 1 chr1 1792666 1796146 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpp6sl5ld2/f1.bed -b /tmp/tmpp6sl5ld2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3407729 3413602 a 0 + 1 chr1 4152160 4156364 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpyqd4mmtc/f1.bed -b /tmp/tmpyqd4mmtc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8386747 8395629 a 0 - 1 chr18 9983725 9988212 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqv7piac9/f1.bed -b /tmp/tmpqv7piac9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2516707 2518765 a 0 + 1 chr11 316501 325622 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4rjotjyf/f1.bed -b /tmp/tmp4rjotjyf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2659908 2661919 a 0 - 1 chr1 439373 444228 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpm1ybd2ag/f1.bed -b /tmp/tmpm1ybd2ag/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 8365 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2jynb6i4/f1.bed -b /tmp/tmp2jynb6i4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7704606 7709598 a 0 + 1 chr1 8982634 8985201 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpnorq497q/f1.bed -b /tmp/tmpnorq497q/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5311204 5312656 a 0 + 1 chr7 4325191 4328342 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp74di5znw/f1.bed -b /tmp/tmp74di5znw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 10000000 10004097 a 0 + 1 chr5 5829132 5833229 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_dv55ed_/f1.bed -b /tmp/tmp_dv55ed_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8956157 8963247 a 0 + 1 chr1 8137377 8142589 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5ev3t9bt/f1.bed -b /tmp/tmp5ev3t9bt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7398277 7404056 a 0 + 1 chr10 9102282 9111241 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxw5gdm6w/f1.bed -b /tmp/tmpxw5gdm6w/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2 4662 a 0 + 1 chr1 956348 962296 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpg6gtzr_x/f1.bed -b /tmp/tmpg6gtzr_x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2394800 2403742 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4hsdbqzs/f1.bed -b /tmp/tmp4hsdbqzs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5042788 5047576 a 0 + 1 chr1 3236218 3241129 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmphbz6nmls/f1.bed -b /tmp/tmphbz6nmls/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6344490 6346123 a 0 + 1 chr22 3360551 3364156 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpnx67e4qr/f1.bed -b /tmp/tmpnx67e4qr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3500653 3502497 a 0 + 1 chr13 3500653 3507641 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmplv418ejx/f1.bed -b /tmp/tmplv418ejx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2931063 2934136 a 0 + 1 chr3 4026481 4035190 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdwt40z6_/f1.bed -b /tmp/tmpdwt40z6_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3336350 3336352 a 0 + 1 chr1 1871290 1876376 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpvll75w7z/f1.bed -b /tmp/tmpvll75w7z/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3878101 3886052 a 0 + 1 chrY 2058902 2061632 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2qxlhxzi/f1.bed -b /tmp/tmp2qxlhxzi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3731213 3741064 a 0 + 1 chr1 8498355 8508206 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpwsi2xkx4/f1.bed -b /tmp/tmpwsi2xkx4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9687224 9693803 a 0 - 1 chr22 1984688 1994069 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpay500e8y/f1.bed -b /tmp/tmpay500e8y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3022938 3026646 a 0 - 1 chrX 5290854 5293566 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_3up6hsu/f1.bed -b /tmp/tmp_3up6hsu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5207553 5208549 a 0 - 1 chr4 1707947 1714354 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdq5unjg4/f1.bed -b /tmp/tmpdq5unjg4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 1478 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpckjmlu7b/f1.bed -b /tmp/tmpckjmlu7b/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3612155 3612698 a 0 - 1 chr20 71815 73073 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpyn6bv9qb/f1.bed -b /tmp/tmpyn6bv9qb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2343690 2346287 a 0 + 1 chr2 1955392 1955394 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_geu_jnz/f1.bed -b /tmp/tmp_geu_jnz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9773318 9777635 a 0 + 1 chr3 6679828 6680961 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqvqnd4d8/f1.bed -b /tmp/tmpqvqnd4d8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4521329 4527305 a 0 - 1 chr4 4521329 4523390 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmprgddrf2x/f1.bed -b /tmp/tmprgddrf2x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9991197 10000723 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpcziabdd4/f1.bed -b /tmp/tmpcziabdd4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1771299 1773201 a 0 - 1 chr2 9710778 9718203 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4dq_7ria/f1.bed -b /tmp/tmp4dq_7ria/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8755679 8762071 a 0 - 1 chr1 5901810 5911299 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpob7duw7s/f1.bed -b /tmp/tmpob7duw7s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2516707 2518765 a 0 + 1 chr11 316501 325622 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpliiwf6x0/f1.bed -b /tmp/tmpliiwf6x0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 3323 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqexu4ivi/f1.bed -b /tmp/tmpqexu4ivi/f2.bed Chromosome Start End Name Score Strand 0 chr1 3594 3595 a 0 - 1 chr1 3594 3595 a 0 - Chromosome Start End Name Score Strand 0 chr1 2004232 2013039 a 0 - 1 chr1 4525787 4527956 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpcy5uxt7i/f1.bed -b /tmp/tmpcy5uxt7i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5311204 5312656 a 0 + 1 chr7 4325191 4328342 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgw8efu8q/f1.bed -b /tmp/tmpgw8efu8q/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 - 1 chr2 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4621341 4624937 a 0 + 1 chr1 6439065 6441610 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpc07pen1x/f1.bed -b /tmp/tmpc07pen1x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9214844 9222906 a 0 - 1 chr1 759661 766345 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpt_x39hx2/f1.bed -b /tmp/tmpt_x39hx2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 6319 a 0 - 1 chr1 1 6319 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpcu47llpk/f1.bed -b /tmp/tmpcu47llpk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6787046 6792791 a 0 + 1 chr13 3422415 3431452 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpu5czqzye/f1.bed -b /tmp/tmpu5czqzye/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 1478 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6ym8jmui/f1.bed -b /tmp/tmp6ym8jmui/f2.bed Chromosome Start End Name Score Strand 0 chr1 2185 2186 a 0 - 1 chr1 2185 2186 a 0 - Chromosome Start End Name Score Strand 0 chr1 5207553 5208549 a 0 - 1 chr4 1707947 1714354 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp3tjhh4_u/f1.bed -b /tmp/tmp3tjhh4_u/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9454921 9457343 a 0 - 1 chrX 1183951 1192408 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpfsgt8uy_/f1.bed -b /tmp/tmpfsgt8uy_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6768863 6777175 a 0 + 1 chr1 188149 197267 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpwpz_7ukk/f1.bed -b /tmp/tmpwpz_7ukk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5042788 5047576 a 0 + 1 chr1 3236218 3241129 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2l87nx77/f1.bed -b /tmp/tmp2l87nx77/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7723934 7733188 a 0 + 1 chr5 3925039 3929860 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpuqp7b00s/f1.bed -b /tmp/tmpuqp7b00s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4721057 4727886 a 0 - 1 chr5 4721057 4721924 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp04a6h4cn/f1.bed -b /tmp/tmp04a6h4cn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2931063 2934136 a 0 + 1 chr3 4026481 4035190 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2qfi38h6/f1.bed -b /tmp/tmp2qfi38h6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3916961 3923306 a 0 + 1 chr7 7318402 7327654 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp07n3sota/f1.bed -b /tmp/tmp07n3sota/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6344490 6346123 a 0 + 1 chr22 3360551 3364156 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp7lm4ojio/f1.bed -b /tmp/tmp7lm4ojio/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 416375 424434 a 0 - 1 chr1 8867098 8870107 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp6oljglmb/f1.bed -b /tmp/tmp6oljglmb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9999999 10009043 a 0 + 1 chr12 7330742 7335798 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzhkw2sxh/f1.bed -b /tmp/tmpzhkw2sxh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 547491 550186 a 0 + 1 chr1 4846495 4847584 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpgrygxl1i/f1.bed -b /tmp/tmpgrygxl1i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5214340 5214721 a 0 + 1 chr1 9044347 9044833 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpt_xwdezh/f1.bed -b /tmp/tmpt_xwdezh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9149995 9156611 a 0 + 1 chr1 6496924 6503874 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp08wdu4ga/f1.bed -b /tmp/tmp08wdu4ga/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6344490 6346123 a 0 + 1 chr22 3360551 3364156 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp42sjlool/f1.bed -b /tmp/tmp42sjlool/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8268630 8275159 a 0 + 1 chr2 4632220 4632864 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqkzqlxmd/f1.bed -b /tmp/tmpqkzqlxmd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8211881 8218351 a 0 - 1 chrX 2856323 2862793 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmprnopl3ln/f1.bed -b /tmp/tmprnopl3ln/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4742165 4744548 a 0 - 1 chr9 7002909 7004952 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpp6rdloeu/f1.bed -b /tmp/tmpp6rdloeu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6361394 6363991 a 0 - 1 chrX 3053076 3057181 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpwa1_5alw/f1.bed -b /tmp/tmpwa1_5alw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4621341 4624937 a 0 + 1 chr1 6439065 6441610 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppoyth3nd/f1.bed -b /tmp/tmppoyth3nd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3336350 3336352 a 0 + 1 chr1 1871290 1876376 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpg14q7p91/f1.bed -b /tmp/tmpg14q7p91/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7059099 7066982 a 0 + 1 chr18 5837577 5845460 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpw6_87i66/f1.bed -b /tmp/tmpw6_87i66/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6787046 6792791 a 0 + 1 chr13 3422415 3431452 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppd4b6lfe/f1.bed -b /tmp/tmppd4b6lfe/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9456074 9460229 a 0 + 1 chr1 9945190 9952845 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2o7t_y5j/f1.bed -b /tmp/tmp2o7t_y5j/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 8365 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_t41zzlx/f1.bed -b /tmp/tmp_t41zzlx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2516707 2518765 a 0 + 1 chr11 316501 325622 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpti5ez1pq/f1.bed -b /tmp/tmpti5ez1pq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4721057 4727886 a 0 - 1 chr5 4721057 4721924 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpa9md5vmg/f1.bed -b /tmp/tmpa9md5vmg/f2.bed Chromosome Start End Name Score Strand 0 chr1 3109 3110 a 0 - 1 chr1 3109 3110 a 0 - Chromosome Start End Name Score Strand 0 chr1 1110118 1117083 a 0 + 1 chr1 1792666 1796146 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpurl2gdna/f1.bed -b /tmp/tmpurl2gdna/f2.bed Chromosome Start End Name Score Strand 0 chr1 3099 3100 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 8162 a 0 + 1 chr1 1 8162 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp711e3ujx/f1.bed -b /tmp/tmp711e3ujx/f2.bed Chromosome Start End Name Score Strand 0 chr1 5005 5006 a 0 - 1 chr1 5005 5006 a 0 - Chromosome Start End Name Score Strand 0 chr1 1787794 1791160 a 0 - 1 chr22 7922615 7927015 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpacad3io4/f1.bed -b /tmp/tmpacad3io4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9999999 10002051 a 0 - 1 chr7 361154 370522 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpvb_twckl/f1.bed -b /tmp/tmpvb_twckl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 6319 a 0 - 1 chr1 1 6319 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmppu49nh9_/f1.bed -b /tmp/tmppu49nh9_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 4200 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpa7icrbxf/f1.bed -b /tmp/tmpa7icrbxf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 547491 550186 a 0 + 1 chr1 4846495 4847584 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpces49h3f/f1.bed -b /tmp/tmpces49h3f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7677437 7683382 a 0 - 1 chr4 2544544 2549275 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp5nrs6mag/f1.bed -b /tmp/tmp5nrs6mag/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8386747 8395629 a 0 - 1 chr18 9983725 9988212 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqo4farn0/f1.bed -b /tmp/tmpqo4farn0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr4 6556968 6560472 a 0 - 1 chr9 949853 957777 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpt1ceveud/f1.bed -b /tmp/tmpt1ceveud/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9x2s6e9u/f1.bed -b /tmp/tmp9x2s6e9u/f2.bed ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________________ test_k_nearest[upstream-True-False-last] ___________________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1e.values, d2s.values, d1e.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=True, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:42 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:46 | (and 38 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGMEijDDEAAAx1ALW') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1s.values, d2e.values, d1s.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=True, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:19 | (and 36 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzsl8n995/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzsl8n995/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmiacyeee/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmiacyeee/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmejqo5vl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmejqo5vl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2bjfulum/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2bjfulum/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj_ne31e1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj_ne31e1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa4jaufap/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa4jaufap/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp58f3u71r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp58f3u71r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpidz5_lzw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpidz5_lzw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfjnhz5gl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfjnhz5gl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnvvcnfmt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnvvcnfmt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4day90lt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4day90lt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo3ffttqy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo3ffttqy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmproii4yxd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmproii4yxd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgnw0tiec/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgnw0tiec/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpycltxvuy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpycltxvuy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi3yjrq0_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi3yjrq0_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoljb4hx1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoljb4hx1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpine9gxiz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpine9gxiz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp89rywiih/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp89rywiih/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9i3k2k05/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9i3k2k05/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw060cq8o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw060cq8o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp71ewrqel/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp71ewrqel/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyw9x25y3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyw9x25y3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzefx9jq7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzefx9jq7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmps1ammrg7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps1ammrg7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2jnobvq6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2jnobvq6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplnzrb0ak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplnzrb0ak/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpalhbrmn6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpalhbrmn6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqb015gbj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqb015gbj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmprppjqw3l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprppjqw3l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpelgfu2ig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpelgfu2ig/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5h6lwd9h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5h6lwd9h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr5gur5oz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr5gur5oz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdyt422e_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdyt422e_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplhrybhoy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplhrybhoy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2n6j_a08/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2n6j_a08/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmppyzkjvjf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppyzkjvjf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4imiwt81/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4imiwt81/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi__iwq38/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi__iwq38/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsyvbwg6k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsyvbwg6k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvod1xxcw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvod1xxcw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpais6rqt8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpais6rqt8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzalxn464/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzalxn464/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3cowvclk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3cowvclk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmph8d4d_hy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph8d4d_hy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4pty_b39/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4pty_b39/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjxvwzvrl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjxvwzvrl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpomlxcxm2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpomlxcxm2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpva1ljiyi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpva1ljiyi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsb7tgbnx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsb7tgbnx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkmi_zhp9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkmi_zhp9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkik_9ji4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkik_9ji4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6w44ggs5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6w44ggs5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk27do00_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk27do00_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjkojumi4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjkojumi4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9c58h0nv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9c58h0nv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp42lykn93/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp42lykn93/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5zyegy6j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5zyegy6j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmprym6tuug/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprym6tuug/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeh1z635o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeh1z635o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwfihox_m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwfihox_m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn0d1qig2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn0d1qig2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7nccyy5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7nccyy5d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyg4uw21i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyg4uw21i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdany6g28/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdany6g28/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg9vmx5gu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg9vmx5gu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpja4joet_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpja4joet_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_jekza71/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_jekza71/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpijj4m3qh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpijj4m3qh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplpnh2ej6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplpnh2ej6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj0hd_u9e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj0hd_u9e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpei4zopnx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpei4zopnx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpizne80wq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpizne80wq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmph4lpie26/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph4lpie26/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp076r3n8q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp076r3n8q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz68954vk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz68954vk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpicz6dxll/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpicz6dxll/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_cda2rd1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_cda2rd1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdfpy0iwt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdfpy0iwt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq07e7uxb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq07e7uxb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcsz3g80n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcsz3g80n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_b39vwur/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_b39vwur/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1gdcc9lk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1gdcc9lk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwj735pc7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwj735pc7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_5rj75vx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_5rj75vx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj6t_nhp9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj6t_nhp9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnze5z0yn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnze5z0yn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgc788zhs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgc788zhs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmppe4jus9d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppe4jus9d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptdqy_xaz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptdqy_xaz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsdkgnjfb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsdkgnjfb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvotxa4j3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvotxa4j3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkm7dhwc6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkm7dhwc6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr3jtijfn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr3jtijfn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7191n2ja/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7191n2ja/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe9nceumf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe9nceumf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv3c379e6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv3c379e6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnh0_l1pl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnh0_l1pl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4f0jpeco/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4f0jpeco/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfgpuf0i8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfgpuf0i8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmppoqnwxsw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppoqnwxsw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmph0b2yqz4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph0b2yqz4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphisivh5v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphisivh5v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjt02wj8l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjt02wj8l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl6morj_9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6morj_9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1td5baqd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1td5baqd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcvb5yygf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcvb5yygf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbyifxyk2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbyifxyk2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6ch9k3ft/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ch9k3ft/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp322nit5l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp322nit5l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphij23wxf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphij23wxf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9n698ys7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9n698ys7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpes23b3m4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpes23b3m4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpftm8dt40/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpftm8dt40/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpep6kvs8z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpep6kvs8z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1j9dqi_5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1j9dqi_5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwsyzf3ca/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwsyzf3ca/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0aqo61yv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0aqo61yv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp032g_xk2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp032g_xk2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0yx85iwb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0yx85iwb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxwq17k8l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxwq17k8l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmppkua2kxp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppkua2kxp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplshse5zg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplshse5zg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc8vg76dn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc8vg76dn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo207x6uc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo207x6uc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpinlsgm8d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpinlsgm8d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmyk7cab4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmyk7cab4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_s2offy4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_s2offy4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx5sj09gn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx5sj09gn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkduln_m1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkduln_m1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxdlumkoz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxdlumkoz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxf5ylua7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxf5ylua7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmbaymbh0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmbaymbh0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmprz5_dyly/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprz5_dyly/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdwxkfy74/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdwxkfy74/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmprahl75l5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprahl75l5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi42f2fzw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi42f2fzw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3s5_w15w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3s5_w15w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkarqfn4c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkarqfn4c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnamnmjaj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnamnmjaj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmprhkt9guo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprhkt9guo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpehahhr2r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpehahhr2r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1ayk9u3e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ayk9u3e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvj4tsku4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvj4tsku4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdfydbjed/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdfydbjed/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp962zujah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp962zujah/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvmxxnb56/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvmxxnb56/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvpi9b2ip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvpi9b2ip/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgv5fo_l4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgv5fo_l4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4cyno364/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4cyno364/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4oq2f4fu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4oq2f4fu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1r4q1l3l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1r4q1l3l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfcky31ji/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfcky31ji/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpas_djkyz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpas_djkyz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuu_wpe1l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuu_wpe1l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgz2dnorz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgz2dnorz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp48af51dq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp48af51dq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkif16875/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkif16875/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_1lo2nx4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_1lo2nx4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvr5qodpi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvr5qodpi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl9lfr2hy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl9lfr2hy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqnh1zrl9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqnh1zrl9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqgomytqg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqgomytqg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl0hte9rc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0hte9rc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp52wo7273/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp52wo7273/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4pr5_6ms/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4pr5_6ms/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzydqm0v5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzydqm0v5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmruxodou/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmruxodou/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkfjtkspk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkfjtkspk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgrpk1dzy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgrpk1dzy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpan58gwkp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpan58gwkp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuxo2hskd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuxo2hskd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl8aru_si/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl8aru_si/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbvvkbg2l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbvvkbg2l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmputcfz1bi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmputcfz1bi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9srj1u4d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9srj1u4d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplf2p7fb4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplf2p7fb4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaouxzipm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaouxzipm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi3d8_h7k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi3d8_h7k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv507qg1w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv507qg1w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_ah7ma34/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ah7ma34/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkkatwpnt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkkatwpnt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoxdj3ib3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoxdj3ib3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptil_7y8c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptil_7y8c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm91pll8l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm91pll8l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcf0motke/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcf0motke/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpetccgz6p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpetccgz6p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvszsfiup/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvszsfiup/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy4rkzp8j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy4rkzp8j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9oqrzjl9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9oqrzjl9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgjxsn8mi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgjxsn8mi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp36tz4s62/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36tz4s62/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfppunaqr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfppunaqr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplmy67m0b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplmy67m0b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp17hpvbk0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp17hpvbk0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkqxgf30t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkqxgf30t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9_02dfqy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_02dfqy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwbwdc6xj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwbwdc6xj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpos4kzyvl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpos4kzyvl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb50q_5xa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb50q_5xa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxatq45bx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxatq45bx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbkjw_jmj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbkjw_jmj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpamzk1tw5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpamzk1tw5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoq37fxb0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoq37fxb0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptkl16d8t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptkl16d8t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3y4gb8bk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3y4gb8bk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8_5hn_4g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8_5hn_4g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpca_065oz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpca_065oz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7f6hdkww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7f6hdkww/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxnu0jw7x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxnu0jw7x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptyk55fvk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptyk55fvk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1d8ghllu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1d8ghllu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpztuenu3a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpztuenu3a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp99d90sh2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp99d90sh2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphn3svu84/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphn3svu84/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzq674i53/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzq674i53/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv2rrd_lh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv2rrd_lh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd2ib525i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd2ib525i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcu4nqtgn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcu4nqtgn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpphacv2ge/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpphacv2ge/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdnygdu0u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdnygdu0u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9xp3uf3w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9xp3uf3w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqt77iwme/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqt77iwme/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2mwg6tii/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2mwg6tii/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8vh1xszy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8vh1xszy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp91m3f8ht/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp91m3f8ht/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv77joos3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv77joos3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv5i8nyfn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv5i8nyfn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0fm4ud1y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0fm4ud1y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8gz043qy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8gz043qy/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________________ test_k_nearest[None-False-opposite-last] ___________________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 nearest_how = None, overlap = False, strandedness = 'opposite', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=False, E strandedness='opposite', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:19 E (and 39 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjRRRgBOKMDFg==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplqbvw0m8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplqbvw0m8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqx_wx7c3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqx_wx7c3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphauub4re/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphauub4re/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsv9nop0p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsv9nop0p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4_wznlo1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4_wznlo1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprj71r1bx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprj71r1bx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo1ovw4rb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo1ovw4rb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpizry6rtk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpizry6rtk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1klfjfwa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1klfjfwa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4pu4q680/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4pu4q680/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoij4i2xl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoij4i2xl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu99glwrm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu99glwrm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn3iexvyc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn3iexvyc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3jx8tk28/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3jx8tk28/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy5mi51rg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy5mi51rg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm6c7j0mb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm6c7j0mb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjt4oorr4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjt4oorr4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj7zv8_8a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj7zv8_8a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpru86s8o1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpru86s8o1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbsbulia2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbsbulia2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnrhwdzv_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnrhwdzv_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4pnb6vs_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4pnb6vs_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr4y49de8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr4y49de8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqh1gj_98/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqh1gj_98/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkmiwupf6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkmiwupf6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplhehwu02/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplhehwu02/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx8ykogm_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx8ykogm_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_fo6a1p7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_fo6a1p7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp59sse29m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp59sse29m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoyq0e4et/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoyq0e4et/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptuu4vnr3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptuu4vnr3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuk7jyc8a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuk7jyc8a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt6oiz434/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt6oiz434/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2i9ob3ip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2i9ob3ip/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpop4brv75/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpop4brv75/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0677ruoz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0677ruoz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsc7ugmpo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsc7ugmpo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphtnx983f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphtnx983f/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain37-method_chain37] ___________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:293 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ___________ test_three_in_a_row[strandedness_chain11-method_chain11] ___________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ______________________ test_nearest[upstream-False-False] ______________________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.Start, ocdf.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_ends.values - 1, right_starts.values, right_indexes) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:115 | (and 38 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGMEijDDEAAAx1ALW') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.End) | ^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:118 | (and 39 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiz__vvrj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiz__vvrj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9f7ydhmx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9f7ydhmx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoe_r1qew/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoe_r1qew/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmq9jixyy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmq9jixyy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg2roe6c0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg2roe6c0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj3fl_quk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj3fl_quk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8d1113po/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8d1113po/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7amu69c8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7amu69c8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp06l2gq0k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp06l2gq0k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_m76uufh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_m76uufh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7s5u6h6o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7s5u6h6o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuoz2un4h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuoz2un4h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd_pn__uq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd_pn__uq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy58j54k1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy58j54k1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0gv_0o0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0gv_0o0e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd5zr72z3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd5zr72z3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphz90x4nw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphz90x4nw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt1ygwpyg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt1ygwpyg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxzw48nvk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxzw48nvk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbqlda8fz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbqlda8fz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmtg2bfjx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmtg2bfjx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm3igteh_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm3igteh_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp08ojmj87/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp08ojmj87/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0otmukj1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0otmukj1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8ubuxyc2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ubuxyc2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpit4bgray/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpit4bgray/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphlp5x94h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphlp5x94h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvc0tz8hr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvc0tz8hr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjcfu6y_k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjcfu6y_k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6d2jlfai/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6d2jlfai/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbxmyt7c8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbxmyt7c8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8gz139lu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8gz139lu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_9tm9aiu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_9tm9aiu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpms1csxyj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpms1csxyj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9vlz12fn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9vlz12fn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3cz_zjrn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3cz_zjrn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwxgrfafr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwxgrfafr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8ykk8t7s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ykk8t7s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiy47i_z0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiy47i_z0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeo4c3vu6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeo4c3vu6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7cz67qyn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7cz67qyn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp78saxc2l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp78saxc2l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvksccejd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvksccejd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz9_8890_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz9_8890_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1f9ka8mx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1f9ka8mx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp77xq6jbd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp77xq6jbd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0qxufitp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0qxufitp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqbdsww2_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqbdsww2_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9zh5trgn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9zh5trgn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo4othuzx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo4othuzx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpabwnw_l8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpabwnw_l8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpade8u1nt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpade8u1nt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3tu1z58m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3tu1z58m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm0tjjp5f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm0tjjp5f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf5wvhe8o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf5wvhe8o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5kol0p0z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5kol0p0z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw3fn83kb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw3fn83kb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk6s5ikhu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk6s5ikhu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp056ekzfg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp056ekzfg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwa4_giya/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwa4_giya/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps175og7m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps175og7m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpznkt3rwb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpznkt3rwb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp983kojg9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp983kojg9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpalw_jlc5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpalw_jlc5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpavyw1ao3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpavyw1ao3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0rxvtd82/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0rxvtd82/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnflde5fb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnflde5fb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppaxrm240/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppaxrm240/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprbgd6_6q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprbgd6_6q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn9agg4dg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn9agg4dg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr7bp866d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr7bp866d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqzvuyxsc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqzvuyxsc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_qo4rowa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_qo4rowa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcgspyjo9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcgspyjo9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmposqeo4nu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmposqeo4nu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpetpszi30/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpetpszi30/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkans54ba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkans54ba/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmjdqa09v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmjdqa09v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplwyl8tma/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplwyl8tma/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm1swpiy9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm1swpiy9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd5v3h3dn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd5v3h3dn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptlg26v8o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptlg26v8o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprt9dq8s8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprt9dq8s8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2zcyxk4s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2zcyxk4s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb7nf3mm6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb7nf3mm6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk92l4n64/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk92l4n64/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphxxeqg_v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphxxeqg_v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq9yqn8z3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9yqn8z3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv2qc6yit/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv2qc6yit/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphoofcrqj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphoofcrqj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvgebpib0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvgebpib0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxdzs3hxc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxdzs3hxc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0f0d2kjg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0f0d2kjg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp99p9aq2f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp99p9aq2f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpajacay65/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpajacay65/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvpuh8szl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvpuh8szl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_lmpal6g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_lmpal6g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjb54gtg5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjb54gtg5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl7dpowwh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl7dpowwh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwjido7ag/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwjido7ag/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwwf5aeqp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwwf5aeqp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdn74l7vs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdn74l7vs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp55vy9qn3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp55vy9qn3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp41t4j6vp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp41t4j6vp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6oxn4mwc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6oxn4mwc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7lsg90fr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7lsg90fr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp96gd13e8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp96gd13e8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdw_gb1ol/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdw_gb1ol/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprvoxrql7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprvoxrql7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc6qns61q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc6qns61q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph6rykknb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph6rykknb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp353yqsnq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp353yqsnq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnhdrihg_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnhdrihg_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt61ch4ps/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt61ch4ps/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw1gdlysx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw1gdlysx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk1te6dg4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk1te6dg4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_i62oe7b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_i62oe7b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3of9bcf_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3of9bcf_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd2cjol8c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd2cjol8c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfv2sjesa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfv2sjesa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdlyt6wg9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdlyt6wg9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppf9_3esj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppf9_3esj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd7j9jf72/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd7j9jf72/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5rfm2yrh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5rfm2yrh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyad9lz3j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyad9lz3j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzq6j_tep/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzq6j_tep/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6zr1fhbs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6zr1fhbs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx8tsnp_f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx8tsnp_f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3wu2_esl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3wu2_esl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpieui56or/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpieui56or/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy7nzpf4h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy7nzpf4h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf8z9thw5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf8z9thw5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4okgxbaj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4okgxbaj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj9m2xtza/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj9m2xtza/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptghskndo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptghskndo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkoanpzxn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkoanpzxn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppmvewbzd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppmvewbzd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa2bet80s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa2bet80s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5pv7t8t0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5pv7t8t0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp902fbfhj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp902fbfhj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4dds9hz_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4dds9hz_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppfow8lx_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppfow8lx_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_irca8tj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_irca8tj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ja2anr6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ja2anr6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsfror0_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsfror0_h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpipk_ja_c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpipk_ja_c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwn0fiq11/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwn0fiq11/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpocbuq14m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpocbuq14m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9s5a2ywy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9s5a2ywy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn32af9o0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn32af9o0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyuxcp023/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyuxcp023/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps58uy696/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps58uy696/f2.bed) _____________________ test_k_nearest[None-False-same-last] _____________________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 nearest_how = None, overlap = False, strandedness = 'same', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=False, E strandedness='same', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:19 E (and 38 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1q8_g8ln/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1q8_g8ln/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9mwxo0xg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9mwxo0xg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa_04wbu8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_04wbu8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp8grupj7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp8grupj7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfwg8qlzn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfwg8qlzn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnv8i8eay/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnv8i8eay/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphghylbn2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphghylbn2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd9a2hv73/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd9a2hv73/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjhganud3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjhganud3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpby9lpt9s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpby9lpt9s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp26krbfnh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp26krbfnh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi0bv4eo4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi0bv4eo4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp73cp70mg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp73cp70mg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr9n8sh8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr9n8sh8_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsub3can9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsub3can9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpegpcfxe7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpegpcfxe7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ab5w660/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ab5w660/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain22-method_chain22] ___________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 171 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 | (and 163 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges 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('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ____________ test_three_in_a_row[strandedness_chain5-method_chain5] ____________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/init.py:174 E (and 186 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ___________ test_three_in_a_row[strandedness_chain60-method_chain60] ___________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ______________________ test_nearest[upstream-False-same] _______________________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.Start, ocdf.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_ends.values - 1, right_starts.values, right_indexes) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 103 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGDFEADi2Axc=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.End) | ^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 103 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp77txke8b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp77txke8b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3drav9bh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3drav9bh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6tka_bcd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6tka_bcd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3ggnvgnv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ggnvgnv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv1hrdf5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv1hrdf5d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbqbzh76x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbqbzh76x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa5h1f4mw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa5h1f4mw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc82_6ek3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc82_6ek3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7azzl2o3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7azzl2o3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp586_ucw0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp586_ucw0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmi_malyn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmi_malyn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2yzecgm1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2yzecgm1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw7zdbe6e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw7zdbe6e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfzjaoj50/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfzjaoj50/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwirxsxdz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwirxsxdz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwrfwg556/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwrfwg556/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5j62ogu9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5j62ogu9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaurr64af/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaurr64af/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn4wap03x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn4wap03x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppmjnff6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppmjnff6y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzlz9rj1h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzlz9rj1h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0lk5nw_0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0lk5nw_0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0p57gq02/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0p57gq02/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg7qcvwbr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7qcvwbr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplt2318fs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplt2318fs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsw0j7d2g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsw0j7d2g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl6qexmz5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6qexmz5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjqlw5umg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjqlw5umg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppophlify/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppophlify/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplbhw73uz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplbhw73uz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl29fd3gs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl29fd3gs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpok575quu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpok575quu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj9rarbcb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj9rarbcb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvow4zt34/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvow4zt34/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1xd1oud1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1xd1oud1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphlvi7xci/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphlvi7xci/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4onuk7gm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4onuk7gm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcaiemxkl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcaiemxkl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpijxbuerw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpijxbuerw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpii49id_9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpii49id_9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpawnvc80o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpawnvc80o/f2.bed) ___________ test_three_in_a_row[strandedness_chain51-method_chain51] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 182 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ___________ test_three_in_a_row[strandedness_chain12-method_chain12] ___________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 104 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ____________ test_three_in_a_row[strandedness_chain6-method_chain6] ____________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 177 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ____________________ test_k_nearest[None-False-False-last] _____________________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 nearest_how = None, overlap = False, strandedness = False, ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=False, E strandedness=False, E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:19 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:28 E (and 36 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeevohhna/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeevohhna/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbmtnw480/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbmtnw480/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxgva_jqc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxgva_jqc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplfojaq6u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplfojaq6u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpchxoqjux/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpchxoqjux/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpijeym6zx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpijeym6zx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg2lnnlzi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg2lnnlzi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcy20xcoh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcy20xcoh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpawn_u4hl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpawn_u4hl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7gv3o19m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7gv3o19m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj1adb5jg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj1adb5jg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj8pkyt_y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj8pkyt_y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph7g7eedh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph7g7eedh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpko3d068_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpko3d068_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz0cajs7g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz0cajs7g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkbip32g3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkbip32g3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg2z801em/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg2z801em/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8s5u1ei0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8s5u1ei0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpst_ys8s7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpst_ys8s7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2cfcxn53/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2cfcxn53/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpasbfhfzq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpasbfhfzq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjc_0otyd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjc_0otyd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxlb7h_ty/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxlb7h_ty/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpitsdck54/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpitsdck54/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6mospgyj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6mospgyj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphdfkbhaa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphdfkbhaa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn6iuqutn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn6iuqutn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyqzy4mac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqzy4mac/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9teifel8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9teifel8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwpwlen85/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwpwlen85/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptkfd_a5u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptkfd_a5u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp90_xqao5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp90_xqao5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu9ykh57v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu9ykh57v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6sfyd80r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6sfyd80r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwy1vi1jh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwy1vi1jh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoy2vauyo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoy2vauyo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjwl6dgjy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjwl6dgjy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp95hrr8o0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp95hrr8o0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1j8o48m8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1j8o48m8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzby81i8y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzby81i8y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxqlfihs5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxqlfihs5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxkja11f3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxkja11f3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx6g0fs52/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx6g0fs52/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_t_t0jyr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_t_t0jyr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp319a0qe0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp319a0qe0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpinw0ne8d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpinw0ne8d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnzge9_47/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnzge9_47/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd3cuinpw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd3cuinpw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzbpbdi6x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzbpbdi6x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppq6f4spw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppq6f4spw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3r1m9037/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3r1m9037/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa2bu9jmq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa2bu9jmq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnfxj2_1c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnfxj2_1c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp012n4nds/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp012n4nds/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_pr7xnwx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_pr7xnwx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2a_wajol/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2a_wajol/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptwjbs6ou/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptwjbs6ou/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcv4q7y9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcv4q7y9w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe6d1d0oq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe6d1d0oq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfk51fq00/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfk51fq00/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp8mt1p1q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp8mt1p1q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7nyhe8zj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7nyhe8zj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl4m1rzd0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl4m1rzd0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppxlrhy02/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppxlrhy02/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2myvueq0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2myvueq0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprld5pbk3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprld5pbk3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppt681ioy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppt681ioy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptbkxt5h1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptbkxt5h1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnnnne73x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnnnne73x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp2bevx88/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp2bevx88/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwttdgpvx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwttdgpvx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj7fqs1cz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj7fqs1cz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7o_dlu6c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7o_dlu6c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjwvsubgj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjwvsubgj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp36zjfu1_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36zjfu1_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwqdvtw7x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwqdvtw7x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjxqwih7o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjxqwih7o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0pp4sfir/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0pp4sfir/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc7m4cblf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc7m4cblf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz571i7kr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz571i7kr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw7hj8yfd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw7hj8yfd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa9nl9a_n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa9nl9a_n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj28a61fq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj28a61fq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaeg01vo1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaeg01vo1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmqihz1iv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmqihz1iv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9o7zc6vp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9o7zc6vp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkr8ygq5w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkr8ygq5w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_y2lml0m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_y2lml0m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpajoug7mp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpajoug7mp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_gvvqchy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_gvvqchy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwu2h0u7k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwu2h0u7k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0jmby5vt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0jmby5vt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptpx3opsq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptpx3opsq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp559esi4a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp559esi4a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpngkyjr09/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpngkyjr09/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeq82ulr0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeq82ulr0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3k162gbf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3k162gbf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjrcq35i7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjrcq35i7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1qns_zan/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1qns_zan/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeb3fwdl1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeb3fwdl1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv9lj8fnj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv9lj8fnj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph3x8nj0x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph3x8nj0x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4l292la8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4l292la8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaw1azg3c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaw1azg3c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm269fk5r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm269fk5r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgb8scetc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgb8scetc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp425cg2ev/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp425cg2ev/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyyxqrdrj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyyxqrdrj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnmua7bdv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnmua7bdv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsy7sqw0b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsy7sqw0b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptor8m44v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptor8m44v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzribrifc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzribrifc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsvob7x4o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsvob7x4o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcthfk10m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcthfk10m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp26j33jd0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp26j33jd0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpghdyyu5u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpghdyyu5u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1zskugjo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1zskugjo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbdp1tq1l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbdp1tq1l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptjkt8fp8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptjkt8fp8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvpahtkab/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvpahtkab/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeskab0mj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeskab0mj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpshwbyme_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpshwbyme_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmb2_09s9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmb2_09s9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe6413rv7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe6413rv7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpppa6v_bl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpppa6v_bl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvifzjpsw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvifzjpsw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi9b6i27i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi9b6i27i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2yvnjsla/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2yvnjsla/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3595q8_8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3595q8_8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp99bvjpi3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp99bvjpi3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpox9lw2gt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpox9lw2gt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx0qq0pdf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx0qq0pdf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuh_d9_29/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuh_d9_29/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoplw635q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoplw635q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprx5f4fjd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprx5f4fjd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa_y95smy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_y95smy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsxmkf9rg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsxmkf9rg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdqwnmjw7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdqwnmjw7/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain38-method_chain38] ___________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGAAYigCskGQEQgZGMFSYDEmiCQAXTsEHQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGQAEgxAJgwxMAAAKV8Ckg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ____________________ test_nearest[upstream-False-opposite] _____________________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.End) | ^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 103 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjRRRgBOKMDFg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.Start, ocdf.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_ends.values - 1, right_starts.values, right_indexes) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=False, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 103 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGMEijDDEAAAx1ALW') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwyyun90o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwyyun90o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfd5dj7uj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfd5dj7uj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp94d34u9z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp94d34u9z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5phk0gwo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5phk0gwo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxo5d0tt4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxo5d0tt4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp90s8bifp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp90s8bifp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpscsmv3_3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpscsmv3_3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5bc0saqz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5bc0saqz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1qnidqpm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1qnidqpm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3ss66uma/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ss66uma/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4r71zwci/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4r71zwci/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxicsv348/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxicsv348/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmstwzmjh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmstwzmjh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpduxkdxla/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpduxkdxla/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqzxn6y6o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqzxn6y6o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzptupg__/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzptupg__/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp89rtp45n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp89rtp45n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3m1mp8gz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3m1mp8gz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo_7tn8uh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo_7tn8uh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpanmyprig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpanmyprig/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn14xrtss/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn14xrtss/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcvfg9lk5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcvfg9lk5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxy1kebdl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxy1kebdl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp63m4ci3q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp63m4ci3q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpogpschoi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpogpschoi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8dz489hu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8dz489hu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphl0000o5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphl0000o5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd7cbbpmq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd7cbbpmq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_czhip98/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_czhip98/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpge1wo7gc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpge1wo7gc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0ot95ed3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ot95ed3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_c5seqt5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_c5seqt5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyb4wrxp_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyb4wrxp_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2o395qu8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2o395qu8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw7sx1p4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw7sx1p4v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0jeggppl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0jeggppl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkz2s_t0c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkz2s_t0c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsr9gw1ej/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsr9gw1ej/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwsvy90r4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwsvy90r4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6i23wlxl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6i23wlxl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzv1nv8gh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzv1nv8gh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv0n8vlhy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv0n8vlhy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppqd7vh8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppqd7vh8_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuuwtcmz4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuuwtcmz4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1vscwltp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1vscwltp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprkxx6a56/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprkxx6a56/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp41k1bfpi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp41k1bfpi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvs59zb2c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvs59zb2c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp79t7l4qp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp79t7l4qp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_7tjx9pc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7tjx9pc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcyhtvkn_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcyhtvkn_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpspbqs1dn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpspbqs1dn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5ih_coxg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ih_coxg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpalqh2rg_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpalqh2rg_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmm52hs6u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmm52hs6u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpck10bgib/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpck10bgib/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmporxls39t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmporxls39t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7s687s85/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7s687s85/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2_sjas40/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2_sjas40/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnv9xdq6w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnv9xdq6w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcg58eqfe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcg58eqfe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpshrqtl1l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpshrqtl1l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpflj7ugte/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpflj7ugte/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp21vgcrjf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp21vgcrjf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm7mga80n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm7mga80n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5z4mmjv7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5z4mmjv7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy0_qm9ue/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy0_qm9ue/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg5iozu3n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg5iozu3n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphwklqpba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphwklqpba/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpad3dbwqt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpad3dbwqt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp72yky7aa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp72yky7aa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppywothvr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppywothvr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9mzu64hq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9mzu64hq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqeukm2t7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqeukm2t7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe94ka590/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe94ka590/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnog8_82n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnog8_82n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxyzmin6r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxyzmin6r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbnbrgpvp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbnbrgpvp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3_hiscx4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3_hiscx4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqu2mn_z3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqu2mn_z3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3oyr5jw7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3oyr5jw7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpidnjua09/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpidnjua09/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf7lcxgrc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf7lcxgrc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmapaut7f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmapaut7f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp60pjntvb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp60pjntvb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnm_hj8y2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnm_hj8y2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp68af9pkl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp68af9pkl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfdjy4yn5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfdjy4yn5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_kjcst80/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_kjcst80/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg0015mrr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg0015mrr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp27g7p1pn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp27g7p1pn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8lbtlt25/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8lbtlt25/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6kok5hi7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6kok5hi7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5lu3so36/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5lu3so36/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe56mtuv7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe56mtuv7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxm0p3jcl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxm0p3jcl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpux5wglcs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpux5wglcs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_19lr2o7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_19lr2o7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbs2cph5q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbs2cph5q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxbz8pq6b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxbz8pq6b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnmn0gh3c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnmn0gh3c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf701mjed/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf701mjed/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7vhwc5u8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7vhwc5u8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1zlx4990/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1zlx4990/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg81zraae/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg81zraae/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps8b7le8f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps8b7le8f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmitofi_c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmitofi_c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqvm10omz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqvm10omz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdavoideg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdavoideg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw1g6ynar/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw1g6ynar/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplj4uohsj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplj4uohsj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8b2mipsy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8b2mipsy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxmsn1wu2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxmsn1wu2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpampd_p5w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpampd_p5w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphd9d9nkz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphd9d9nkz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa79bngp4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa79bngp4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl5colwez/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl5colwez/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphi_01hmj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphi_01hmj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfvuqnqrz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfvuqnqrz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp67ql4egb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp67ql4egb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprhexn9g9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprhexn9g9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps1ip419h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps1ip419h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7pm9o483/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7pm9o483/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjm0ccmew/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjm0ccmew/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk1hmjxwy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk1hmjxwy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6ivdtnf7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ivdtnf7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjijof8r6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjijof8r6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxw9i61_0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxw9i61_0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9aloaos2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9aloaos2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfemvosfb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfemvosfb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsrd5gc9a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsrd5gc9a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_hvsye4e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_hvsye4e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdo27rdy7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdo27rdy7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdhvztwpg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdhvztwpg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt5uzdvtg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt5uzdvtg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv_50cfz4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv_50cfz4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2bq12oz2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2bq12oz2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3mlgrh7r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3mlgrh7r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe2t3ma_8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe2t3ma_8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5hs9eag_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5hs9eag_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprcwt0j6h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprcwt0j6h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe7i1wi3b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7i1wi3b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptrvwudz9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptrvwudz9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu0x6_fvv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu0x6_fvv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkb0vett9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkb0vett9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ma143pk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ma143pk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9yyfw0t2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9yyfw0t2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt7tyh0e5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt7tyh0e5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1fhk_yte/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1fhk_yte/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_aj3xufm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_aj3xufm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3prldsme/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3prldsme/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqyov80gr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqyov80gr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwz1uvdps/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwz1uvdps/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuyikuz88/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuyikuz88/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5luaxgv1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5luaxgv1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3peisbbg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3peisbbg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgzomxs3u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgzomxs3u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw2w21lq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw2w21lq2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdchu3w1_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdchu3w1_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplffe6sde/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplffe6sde/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp06msywb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp06msywb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyg21gtyy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyg21gtyy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgc8tra_d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgc8tra_d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp78pa75dl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp78pa75dl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0py491oe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0py491oe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdwelpybv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdwelpybv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpewbmmtgc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpewbmmtgc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx0t_5xui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx0t_5xui/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcx933p3u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcx933p3u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr0m7wdit/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr0m7wdit/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4s5w9odd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4s5w9odd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeb1poqcz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeb1poqcz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsr3pvq7p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsr3pvq7p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqxzxmenu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqxzxmenu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk_73hfr2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_73hfr2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpklbcrc79/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpklbcrc79/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmp91bylg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmp91bylg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3cclh_jc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3cclh_jc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprnyohxwp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprnyohxwp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph4i28ide/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph4i28ide/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpov7h6xrn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpov7h6xrn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr5ob9m5f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr5ob9m5f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkzwbm5ia/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkzwbm5ia/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_8nw1t39/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_8nw1t39/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2d64zgp8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2d64zgp8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpft7axli9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpft7axli9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpegfl6nko/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpegfl6nko/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprh3deqn1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprh3deqn1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7dqtb68t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7dqtb68t/f2.bed) ___________ test_three_in_a_row[strandedness_chain23-method_chain23] ___________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGAAYkcmMMnACOYDIZjLCGGAIQMATxkD3Q==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ___________ test_three_in_a_row[strandedness_chain61-method_chain61] ___________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 101 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ___________ test_three_in_a_row[strandedness_chain52-method_chain52] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 179 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ___________________ test_k_nearest[None-True-opposite-last] ____________________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 nearest_how = None, overlap = True, strandedness = 'opposite', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=True, E strandedness='opposite', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:19 E (and 38 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjRRRgBOKMDFg==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppytarq4n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppytarq4n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjaejbfg8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjaejbfg8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy5h2i5r8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy5h2i5r8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps03k5dgp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps03k5dgp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf808c2hr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf808c2hr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv7plvgv4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv7plvgv4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3cjjjuhp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3cjjjuhp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbjf_lxrr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbjf_lxrr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjg2r6hp1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjg2r6hp1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuv9gmfyb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuv9gmfyb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0m1z808q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0m1z808q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmph1_5xhkx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph1_5xhkx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxp34j7yx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxp34j7yx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0pbs5dn6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0pbs5dn6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpczbmj0ic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpczbmj0ic/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgezz1ly_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgezz1ly_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphgkpwu29/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphgkpwu29/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyln80wtp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyln80wtp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvnd9egen/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvnd9egen/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9dnxtwqx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9dnxtwqx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpglkgva43/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpglkgva43/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8007p69d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8007p69d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu6q279b8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu6q279b8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4n6zgjy3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4n6zgjy3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz8f526kk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz8f526kk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiaeldr5t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiaeldr5t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbq_cnfqv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbq_cnfqv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpquswlyy5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpquswlyy5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw2wwyv53/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw2wwyv53/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk4xgn95i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk4xgn95i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp02m7fhjx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp02m7fhjx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6bj0wmgy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6bj0wmgy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt2rgfuph/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt2rgfuph/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyuo2hdja/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyuo2hdja/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbmridcob/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbmridcob/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpssojnutx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpssojnutx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpba87x173/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpba87x173/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp00lfrtbu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00lfrtbu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq24bon5x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq24bon5x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg8bphsrw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg8bphsrw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3sw0lf2l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3sw0lf2l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwkwrsehh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwkwrsehh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmgu31r3t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmgu31r3t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptsqkzc57/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptsqkzc57/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_bmpi9sp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_bmpi9sp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd7lxwfdk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd7lxwfdk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptes94s2v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptes94s2v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp55kguscc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp55kguscc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmd_kxz2i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmd_kxz2i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7t4ltq_4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7t4ltq_4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj0p7nd1f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj0p7nd1f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbghpkto6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbghpkto6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdbx2smzo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdbx2smzo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8849v85x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8849v85x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpms5y5mve/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpms5y5mve/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdlwpcu7s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdlwpcu7s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq_eluwnc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq_eluwnc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy57o0z4q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy57o0z4q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0044kdfn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0044kdfn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1hmisqsr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1hmisqsr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpun8z01i6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpun8z01i6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp07m1mdg_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp07m1mdg_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd7k2webt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd7k2webt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3jf8ioqi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3jf8ioqi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1n0irvju/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1n0irvju/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6yt9xk5j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6yt9xk5j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmputrmkndn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmputrmkndn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoov16owr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoov16owr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbpi0l_ly/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbpi0l_ly/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9ervyejf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ervyejf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppxy2j9sv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppxy2j9sv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyf4svar2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyf4svar2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm2gouo2a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm2gouo2a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnw9segff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnw9segff/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1nauta5q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1nauta5q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpodtiq09f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpodtiq09f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplzc7pcj3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplzc7pcj3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp55lvp0ro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp55lvp0ro/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg5saxr7y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg5saxr7y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpadctemf1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpadctemf1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx8bm52m9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx8bm52m9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp39gm7lac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp39gm7lac/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpda7syxxb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpda7syxxb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpteh022k5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpteh022k5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp95f2c853/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp95f2c853/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7p33y6hd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7p33y6hd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv3sgjy95/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv3sgjy95/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7y07h7hy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7y07h7hy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7zdqbszp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7zdqbszp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3g612xls/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3g612xls/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7bm94ll0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7bm94ll0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuayj72jf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuayj72jf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaa3qtk4p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaa3qtk4p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy5f9v8gh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy5f9v8gh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp39bx692n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp39bx692n/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain13-method_chain13] ___________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E /usr/lib/python3/dist-packages/pandas/core/common.py:143 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') _____________________ test_k_nearest[None-True-same-last] ______________________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 nearest_how = None, overlap = True, strandedness = 'same', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=True, E strandedness='same', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:19 E (and 39 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp70rdnmtp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp70rdnmtp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpas5tn7uz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpas5tn7uz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptbwcta6x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptbwcta6x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy7h3wrh6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy7h3wrh6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqrllvyum/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqrllvyum/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5x_j4bo7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5x_j4bo7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpous0h86i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpous0h86i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdljuzdga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdljuzdga/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv2pzovgg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv2pzovgg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq28rzwni/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq28rzwni/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpypnquw2w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpypnquw2w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpztehda9n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpztehda9n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5t6dr_z1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5t6dr_z1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmps5_pptdb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps5_pptdb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcc3i51nm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcc3i51nm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpea3s0svj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpea3s0svj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpriylgb9h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpriylgb9h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpimg6d5_4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpimg6d5_4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf2g7igeq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf2g7igeq/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ____________________________ test_set_union[False] _____________________________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:134: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:149: in test_set_union result = gr.set_union(gr2, strandedness=strandedness) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_set_union( E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd cat /tmp/tmp07tc8cum/f1.bed /tmp/tmp07tc8cum/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0a6wkjze/f1.bed /tmp/tmp0a6wkjze/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9una7i57/f1.bed /tmp/tmp9una7i57/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxv4ywyes/f1.bed /tmp/tmpxv4ywyes/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8f30__0b/f1.bed /tmp/tmp8f30__0b/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpedbzzftc/f1.bed /tmp/tmpedbzzftc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfi3brv5z/f1.bed /tmp/tmpfi3brv5z/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi5vazwu7/f1.bed /tmp/tmpi5vazwu7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpe2lgmqzh/f1.bed /tmp/tmpe2lgmqzh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplwl79t8g/f1.bed /tmp/tmplwl79t8g/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzw984_ib/f1.bed /tmp/tmpzw984_ib/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpje6kht3o/f1.bed /tmp/tmpje6kht3o/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp60t11qt5/f1.bed /tmp/tmp60t11qt5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkwfw9dwt/f1.bed /tmp/tmpkwfw9dwt/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpujefbs9t/f1.bed /tmp/tmpujefbs9t/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppwgpwbte/f1.bed /tmp/tmppwgpwbte/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgmo119c5/f1.bed /tmp/tmpgmo119c5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplls_v6lm/f1.bed /tmp/tmplls_v6lm/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0rfydgro/f1.bed /tmp/tmp0rfydgro/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw32ldbdz/f1.bed /tmp/tmpw32ldbdz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpg9_g07o7/f1.bed /tmp/tmpg9_g07o7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppkds7848/f1.bed /tmp/tmppkds7848/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu5hxv9t1/f1.bed /tmp/tmpu5hxv9t1/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpabiil31f/f1.bed /tmp/tmpabiil31f/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpg0jkcq4a/f1.bed /tmp/tmpg0jkcq4a/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkatdigz_/f1.bed /tmp/tmpkatdigz_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxa4w3jqq/f1.bed /tmp/tmpxa4w3jqq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc5bwrjlz/f1.bed /tmp/tmpc5bwrjlz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvk9_v2y9/f1.bed /tmp/tmpvk9_v2y9/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn26bro_9/f1.bed /tmp/tmpn26bro_9/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps0u1621b/f1.bed /tmp/tmps0u1621b/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmoxdwp_k/f1.bed /tmp/tmpmoxdwp_k/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdj1zvj1p/f1.bed /tmp/tmpdj1zvj1p/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6by1v805/f1.bed /tmp/tmp6by1v805/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpq_r7x7nu/f1.bed /tmp/tmpq_r7x7nu/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7477ksex/f1.bed /tmp/tmp7477ksex/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpriqtxo45/f1.bed /tmp/tmpriqtxo45/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpd6_uccnw/f1.bed /tmp/tmpd6_uccnw/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp67543flx/f1.bed /tmp/tmp67543flx/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfkoac7f4/f1.bed /tmp/tmpfkoac7f4/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvusi8m9d/f1.bed /tmp/tmpvusi8m9d/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps4hum0v8/f1.bed /tmp/tmps4hum0v8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz47riwon/f1.bed /tmp/tmpz47riwon/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppm5c52b9/f1.bed /tmp/tmppm5c52b9/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwxx873ux/f1.bed /tmp/tmpwxx873ux/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2t7w_c0c/f1.bed /tmp/tmp2t7w_c0c/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpskz39q9f/f1.bed /tmp/tmpskz39q9f/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7iz0sjdm/f1.bed /tmp/tmp7iz0sjdm/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp895oj49y/f1.bed /tmp/tmp895oj49y/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjyah9ddj/f1.bed /tmp/tmpjyah9ddj/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphraqguv2/f1.bed /tmp/tmphraqguv2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0skd9244/f1.bed /tmp/tmp0skd9244/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu6t_q1eo/f1.bed /tmp/tmpu6t_q1eo/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdvu6pyyv/f1.bed /tmp/tmpdvu6pyyv/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1q_v81c9/f1.bed /tmp/tmp1q_v81c9/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpch5ygqmo/f1.bed /tmp/tmpch5ygqmo/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpg9ak7y_w/f1.bed /tmp/tmpg9ak7y_w/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqwq3u3uc/f1.bed /tmp/tmpqwq3u3uc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4wzdt_u5/f1.bed /tmp/tmp4wzdt_u5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcutkj20d/f1.bed /tmp/tmpcutkj20d/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsyr0lrkp/f1.bed /tmp/tmpsyr0lrkp/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphvxx0c3b/f1.bed /tmp/tmphvxx0c3b/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdugyx046/f1.bed /tmp/tmpdugyx046/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpktu4z93e/f1.bed /tmp/tmpktu4z93e/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxykz627v/f1.bed /tmp/tmpxykz627v/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgg2mkfvx/f1.bed /tmp/tmpgg2mkfvx/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj745ooee/f1.bed /tmp/tmpj745ooee/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl_sdoef4/f1.bed /tmp/tmpl_sdoef4/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppgxmb89i/f1.bed /tmp/tmppgxmb89i/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6r7qo0c2/f1.bed /tmp/tmp6r7qo0c2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpabdgcbqr/f1.bed /tmp/tmpabdgcbqr/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw_1vgvub/f1.bed /tmp/tmpw_1vgvub/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuqjgrj6l/f1.bed /tmp/tmpuqjgrj6l/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjkmh47px/f1.bed /tmp/tmpjkmh47px/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp65w3ndmh/f1.bed /tmp/tmp65w3ndmh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpr1p_aexd/f1.bed /tmp/tmpr1p_aexd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2o_m2wkz/f1.bed /tmp/tmp2o_m2wkz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpx472_w23/f1.bed /tmp/tmpx472_w23/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyo0t94k_/f1.bed /tmp/tmpyo0t94k_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfoq3c25u/f1.bed /tmp/tmpfoq3c25u/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpniv8olye/f1.bed /tmp/tmpniv8olye/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzehgffp5/f1.bed /tmp/tmpzehgffp5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu5mdh42l/f1.bed /tmp/tmpu5mdh42l/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph6_wxerr/f1.bed /tmp/tmph6_wxerr/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2qjnwjhq/f1.bed /tmp/tmp2qjnwjhq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl3sexgcs/f1.bed /tmp/tmpl3sexgcs/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpm3k3fz72/f1.bed /tmp/tmpm3k3fz72/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp740b69u8/f1.bed /tmp/tmp740b69u8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcszus9dy/f1.bed /tmp/tmpcszus9dy/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqrdi58fp/f1.bed /tmp/tmpqrdi58fp/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyz9y_0nh/f1.bed /tmp/tmpyz9y_0nh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz1itu1i4/f1.bed /tmp/tmpz1itu1i4/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp50fb_9b6/f1.bed /tmp/tmp50fb_9b6/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfdezeqyb/f1.bed /tmp/tmpfdezeqyb/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp54akx0n7/f1.bed /tmp/tmp54akx0n7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpad_e80q3/f1.bed /tmp/tmpad_e80q3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpd9vvabe4/f1.bed /tmp/tmpd9vvabe4/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpceqlt45w/f1.bed /tmp/tmpceqlt45w/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvk7c7rmc/f1.bed /tmp/tmpvk7c7rmc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpea15hu5d/f1.bed /tmp/tmpea15hu5d/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi0_r8fz8/f1.bed /tmp/tmpi0_r8fz8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqclnc80x/f1.bed /tmp/tmpqclnc80x/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl4ykwa3f/f1.bed /tmp/tmpl4ykwa3f/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxfqhtydl/f1.bed /tmp/tmpxfqhtydl/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2g79i7o0/f1.bed /tmp/tmp2g79i7o0/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc83erzih/f1.bed /tmp/tmpc83erzih/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfd5yqce4/f1.bed /tmp/tmpfd5yqce4/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7e9dhqv1/f1.bed /tmp/tmp7e9dhqv1/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqlfqydwn/f1.bed /tmp/tmpqlfqydwn/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxhdnum4n/f1.bed /tmp/tmpxhdnum4n/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbmrpouft/f1.bed /tmp/tmpbmrpouft/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpprrwy5hs/f1.bed /tmp/tmpprrwy5hs/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbj95f3w5/f1.bed /tmp/tmpbj95f3w5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuzz5ebie/f1.bed /tmp/tmpuzz5ebie/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp37k279wk/f1.bed /tmp/tmp37k279wk/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8g3lldyl/f1.bed /tmp/tmp8g3lldyl/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxtpsu3ri/f1.bed /tmp/tmpxtpsu3ri/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpg_xgqbkx/f1.bed /tmp/tmpg_xgqbkx/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpaj4agnq7/f1.bed /tmp/tmpaj4agnq7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdi5my62h/f1.bed /tmp/tmpdi5my62h/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvcqqotek/f1.bed /tmp/tmpvcqqotek/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpze3dthks/f1.bed /tmp/tmpze3dthks/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuzb_wor3/f1.bed /tmp/tmpuzb_wor3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvjpm8q52/f1.bed /tmp/tmpvjpm8q52/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph930_iv9/f1.bed /tmp/tmph930_iv9/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpoliujcth/f1.bed /tmp/tmpoliujcth/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf9a5kin1/f1.bed /tmp/tmpf9a5kin1/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf8qjqpm8/f1.bed /tmp/tmpf8qjqpm8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppy_gldpo/f1.bed /tmp/tmppy_gldpo/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwe5fyz7f/f1.bed /tmp/tmpwe5fyz7f/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxnyaocbb/f1.bed /tmp/tmpxnyaocbb/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4ytb12hs/f1.bed /tmp/tmp4ytb12hs/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfhbp2rjs/f1.bed /tmp/tmpfhbp2rjs/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1zszhjyy/f1.bed /tmp/tmp1zszhjyy/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppidiux5w/f1.bed /tmp/tmppidiux5w/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzww6ff39/f1.bed /tmp/tmpzww6ff39/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3thdnwm4/f1.bed /tmp/tmp3thdnwm4/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4tnuzv3x/f1.bed /tmp/tmp4tnuzv3x/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprf5uru1n/f1.bed /tmp/tmprf5uru1n/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkpvvau8w/f1.bed /tmp/tmpkpvvau8w/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbvvr_gt_/f1.bed /tmp/tmpbvvr_gt_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt7pwnz6t/f1.bed /tmp/tmpt7pwnz6t/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwnsan0wo/f1.bed /tmp/tmpwnsan0wo/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_9ylzzy7/f1.bed /tmp/tmp_9ylzzy7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1r3onh8v/f1.bed /tmp/tmp1r3onh8v/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps4dbcxix/f1.bed /tmp/tmps4dbcxix/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpp3te3yxs/f1.bed /tmp/tmpp3te3yxs/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmponlhlkne/f1.bed /tmp/tmponlhlkne/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2gku2kyy/f1.bed /tmp/tmp2gku2kyy/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmfr2790k/f1.bed /tmp/tmpmfr2790k/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwuyan_s2/f1.bed /tmp/tmpwuyan_s2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphluicmc8/f1.bed /tmp/tmphluicmc8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3k7le043/f1.bed /tmp/tmp3k7le043/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu2ww2thh/f1.bed /tmp/tmpu2ww2thh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5n7imays/f1.bed /tmp/tmp5n7imays/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7ie5vn1a/f1.bed /tmp/tmp7ie5vn1a/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfimjbqfy/f1.bed /tmp/tmpfimjbqfy/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpr0gu6ohb/f1.bed /tmp/tmpr0gu6ohb/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpygzx3bj6/f1.bed /tmp/tmpygzx3bj6/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp32y8cn0r/f1.bed /tmp/tmp32y8cn0r/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp65idaejf/f1.bed /tmp/tmp65idaejf/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpa8j79jxu/f1.bed /tmp/tmpa8j79jxu/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu0c9v5f9/f1.bed /tmp/tmpu0c9v5f9/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5pufs3fm/f1.bed /tmp/tmp5pufs3fm/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8v9q6j64/f1.bed /tmp/tmp8v9q6j64/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprvnt0ynr/f1.bed /tmp/tmprvnt0ynr/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpv6sv7po6/f1.bed /tmp/tmpv6sv7po6/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptn__a9gw/f1.bed /tmp/tmptn__a9gw/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsto_vphd/f1.bed /tmp/tmpsto_vphd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw33a_6zu/f1.bed /tmp/tmpw33a_6zu/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph08b0x2w/f1.bed /tmp/tmph08b0x2w/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpolb6eo9i/f1.bed /tmp/tmpolb6eo9i/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsn4qmz15/f1.bed /tmp/tmpsn4qmz15/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8ll5dt6w/f1.bed /tmp/tmp8ll5dt6w/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnvg9cwry/f1.bed /tmp/tmpnvg9cwry/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpga46erra/f1.bed /tmp/tmpga46erra/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0u28nldh/f1.bed /tmp/tmp0u28nldh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpd_6ocgde/f1.bed /tmp/tmpd_6ocgde/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0tpz86u7/f1.bed /tmp/tmp0tpz86u7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpiqhf_ycs/f1.bed /tmp/tmpiqhf_ycs/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyynt54u3/f1.bed /tmp/tmpyynt54u3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpoh5s1h9h/f1.bed /tmp/tmpoh5s1h9h/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2k82dqyo/f1.bed /tmp/tmp2k82dqyo/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsg3dyy40/f1.bed /tmp/tmpsg3dyy40/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplfxc9f0a/f1.bed /tmp/tmplfxc9f0a/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmya0kbrf/f1.bed /tmp/tmpmya0kbrf/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpumxige6r/f1.bed /tmp/tmpumxige6r/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppvnc9696/f1.bed /tmp/tmppvnc9696/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplpagaqjd/f1.bed /tmp/tmplpagaqjd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpld7xtcbv/f1.bed /tmp/tmpld7xtcbv/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9aapqib_/f1.bed /tmp/tmp9aapqib_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz54xuwvj/f1.bed /tmp/tmpz54xuwvj/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpplli6mvz/f1.bed /tmp/tmpplli6mvz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpssk7kp7x/f1.bed /tmp/tmpssk7kp7x/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpk6k5qgkr/f1.bed /tmp/tmpk6k5qgkr/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpq1gnymr9/f1.bed /tmp/tmpq1gnymr9/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxwjrne3m/f1.bed /tmp/tmpxwjrne3m/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnd2cdhw6/f1.bed /tmp/tmpnd2cdhw6/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0hql5zxg/f1.bed /tmp/tmp0hql5zxg/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9xkz8ih2/f1.bed /tmp/tmp9xkz8ih2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn2ug97n6/f1.bed /tmp/tmpn2ug97n6/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgtor5jcq/f1.bed /tmp/tmpgtor5jcq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpo__rybe3/f1.bed /tmp/tmpo__rybe3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5a257_zd/f1.bed /tmp/tmp5a257_zd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpenl_xuif/f1.bed /tmp/tmpenl_xuif/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbscudu3l/f1.bed /tmp/tmpbscudu3l/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_3m5t5vh/f1.bed /tmp/tmp_3m5t5vh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2sf53ofc/f1.bed /tmp/tmp2sf53ofc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsmgkvde4/f1.bed /tmp/tmpsmgkvde4/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdxrcfau1/f1.bed /tmp/tmpdxrcfau1/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj0zyq6pr/f1.bed /tmp/tmpj0zyq6pr/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp25eauqe7/f1.bed /tmp/tmp25eauqe7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkc9wvz4x/f1.bed /tmp/tmpkc9wvz4x/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1paf1gd5/f1.bed /tmp/tmp1paf1gd5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3kkwu5wy/f1.bed /tmp/tmp3kkwu5wy/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdxh3ggvi/f1.bed /tmp/tmpdxh3ggvi/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvk4ylhte/f1.bed /tmp/tmpvk4ylhte/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp710zg2ed/f1.bed /tmp/tmp710zg2ed/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptw0_4a7z/f1.bed /tmp/tmptw0_4a7z/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvo2fkrg3/f1.bed /tmp/tmpvo2fkrg3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbde3db_7/f1.bed /tmp/tmpbde3db_7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc__i1l6x/f1.bed /tmp/tmpc__i1l6x/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp10t4v87n/f1.bed /tmp/tmp10t4v87n/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp90txdyy8/f1.bed /tmp/tmp90txdyy8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphrlu6vjs/f1.bed /tmp/tmphrlu6vjs/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpon_cvl1h/f1.bed /tmp/tmpon_cvl1h/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpor4cruc7/f1.bed /tmp/tmpor4cruc7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn7vrzcrs/f1.bed /tmp/tmpn7vrzcrs/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyn0qsxmh/f1.bed /tmp/tmpyn0qsxmh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzyni918_/f1.bed /tmp/tmpzyni918_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9vt912ab/f1.bed /tmp/tmp9vt912ab/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwmfivkxz/f1.bed /tmp/tmpwmfivkxz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4scjjya_/f1.bed /tmp/tmp4scjjya_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9gu75qhn/f1.bed /tmp/tmp9gu75qhn/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpexips2pp/f1.bed /tmp/tmpexips2pp/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvbriz573/f1.bed /tmp/tmpvbriz573/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2zwe_ab5/f1.bed /tmp/tmp2zwe_ab5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0i16kylx/f1.bed /tmp/tmp0i16kylx/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpy23lyonh/f1.bed /tmp/tmpy23lyonh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpatmsv1ck/f1.bed /tmp/tmpatmsv1ck/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgipor9c8/f1.bed /tmp/tmpgipor9c8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpg9gk4h1i/f1.bed /tmp/tmpg9gk4h1i/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3nr8dp2d/f1.bed /tmp/tmp3nr8dp2d/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2z1vtuvw/f1.bed /tmp/tmp2z1vtuvw/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0hmhgj28/f1.bed /tmp/tmp0hmhgj28/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1zsgj92h/f1.bed /tmp/tmp1zsgj92h/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5kmyqs3y/f1.bed /tmp/tmp5kmyqs3y/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7h2nc9u8/f1.bed /tmp/tmp7h2nc9u8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxxavse72/f1.bed /tmp/tmpxxavse72/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn0pbmoxh/f1.bed /tmp/tmpn0pbmoxh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpadghbagc/f1.bed /tmp/tmpadghbagc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwcfimc74/f1.bed /tmp/tmpwcfimc74/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmz8p1n21/f1.bed /tmp/tmpmz8p1n21/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpakfeq4jc/f1.bed /tmp/tmpakfeq4jc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz1akx6eo/f1.bed /tmp/tmpz1akx6eo/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpoqfqcb_q/f1.bed /tmp/tmpoqfqcb_q/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp40mgezv_/f1.bed /tmp/tmp40mgezv_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnil2z9re/f1.bed /tmp/tmpnil2z9re/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpg440bo0v/f1.bed /tmp/tmpg440bo0v/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcuo5wezo/f1.bed /tmp/tmpcuo5wezo/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9nc7jl03/f1.bed /tmp/tmp9nc7jl03/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp93daxeyu/f1.bed /tmp/tmp93daxeyu/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgqvyrb7_/f1.bed /tmp/tmpgqvyrb7_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpr_iepw61/f1.bed /tmp/tmpr_iepw61/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphib6ad6o/f1.bed /tmp/tmphib6ad6o/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjcyea_c5/f1.bed /tmp/tmpjcyea_c5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvu1fdt7f/f1.bed /tmp/tmpvu1fdt7f/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcwdrwc56/f1.bed /tmp/tmpcwdrwc56/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbg_n3ffg/f1.bed /tmp/tmpbg_n3ffg/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1mxfyq4q/f1.bed /tmp/tmp1mxfyq4q/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpygs522zc/f1.bed /tmp/tmpygs522zc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmovnpn37/f1.bed /tmp/tmpmovnpn37/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5lm435eh/f1.bed /tmp/tmp5lm435eh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprpxbma25/f1.bed /tmp/tmprpxbma25/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvrykwwwf/f1.bed /tmp/tmpvrykwwwf/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz6fg88pb/f1.bed /tmp/tmpz6fg88pb/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4sw8jti8/f1.bed /tmp/tmp4sw8jti8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp92t02l_l/f1.bed /tmp/tmp92t02l_l/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_tvvq7qq/f1.bed /tmp/tmp_tvvq7qq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzkiz4ivf/f1.bed /tmp/tmpzkiz4ivf/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpigvfwbyy/f1.bed /tmp/tmpigvfwbyy/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppqsaeea0/f1.bed /tmp/tmppqsaeea0/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4k_57l64/f1.bed /tmp/tmp4k_57l64/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpv68k60pr/f1.bed /tmp/tmpv68k60pr/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4u0l9jpd/f1.bed /tmp/tmp4u0l9jpd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcr834evt/f1.bed /tmp/tmpcr834evt/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp25btxawf/f1.bed /tmp/tmp25btxawf/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3g83r056/f1.bed /tmp/tmp3g83r056/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_s9md8y1/f1.bed /tmp/tmp_s9md8y1/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpoks1wne5/f1.bed /tmp/tmpoks1wne5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp02b5ct65/f1.bed /tmp/tmp02b5ct65/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp92uo8mgx/f1.bed /tmp/tmp92uo8mgx/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxyx1gfto/f1.bed /tmp/tmpxyx1gfto/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp33my7zyz/f1.bed /tmp/tmp33my7zyz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjk3mcw7f/f1.bed /tmp/tmpjk3mcw7f/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgg4mwuz2/f1.bed /tmp/tmpgg4mwuz2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfrjotrhq/f1.bed /tmp/tmpfrjotrhq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpv00p7j17/f1.bed /tmp/tmpv00p7j17/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpoqy5qdq2/f1.bed /tmp/tmpoqy5qdq2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcjnpkn_l/f1.bed /tmp/tmpcjnpkn_l/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgcv0hu8n/f1.bed /tmp/tmpgcv0hu8n/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpaxxi_kqm/f1.bed /tmp/tmpaxxi_kqm/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7feknwv3/f1.bed /tmp/tmp7feknwv3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpb3cm7nyj/f1.bed /tmp/tmpb3cm7nyj/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp535pu9af/f1.bed /tmp/tmp535pu9af/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuw6573r8/f1.bed /tmp/tmpuw6573r8/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc4lgnc7w/f1.bed /tmp/tmpc4lgnc7w/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn_wpsdkg/f1.bed /tmp/tmpn_wpsdkg/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpe3xtyhvk/f1.bed /tmp/tmpe3xtyhvk/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxwh4rnop/f1.bed /tmp/tmpxwh4rnop/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpah60fa_4/f1.bed /tmp/tmpah60fa_4/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpepvk17xd/f1.bed /tmp/tmpepvk17xd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp37r28ek3/f1.bed /tmp/tmp37r28ek3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptvy1o_x1/f1.bed /tmp/tmptvy1o_x1/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp509xly3_/f1.bed /tmp/tmp509xly3_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwar1irwq/f1.bed /tmp/tmpwar1irwq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_m9lsmpn/f1.bed /tmp/tmp_m9lsmpn/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9ubp7fop/f1.bed /tmp/tmp9ubp7fop/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5wsax_ky/f1.bed /tmp/tmp5wsax_ky/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvh_esi39/f1.bed /tmp/tmpvh_esi39/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6ukj3umk/f1.bed /tmp/tmp6ukj3umk/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbktr3plb/f1.bed /tmp/tmpbktr3plb/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2jnunjn3/f1.bed /tmp/tmp2jnunjn3/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwcf5ujyp/f1.bed /tmp/tmpwcf5ujyp/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwkc4wye9/f1.bed /tmp/tmpwkc4wye9/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcttyzbol/f1.bed /tmp/tmpcttyzbol/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc66ikdm6/f1.bed /tmp/tmpc66ikdm6/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp11c_zice/f1.bed /tmp/tmp11c_zice/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_wcm5fue/f1.bed /tmp/tmp_wcm5fue/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfc2i8p8k/f1.bed /tmp/tmpfc2i8p8k/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl6aa12yu/f1.bed /tmp/tmpl6aa12yu/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpy8baksmz/f1.bed /tmp/tmpy8baksmz/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2er95k1u/f1.bed /tmp/tmp2er95k1u/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnqiohk_t/f1.bed /tmp/tmpnqiohk_t/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_hdb13n2/f1.bed /tmp/tmp_hdb13n2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsyw6lq__/f1.bed /tmp/tmpsyw6lq__/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_h8pqsgq/f1.bed /tmp/tmp_h8pqsgq/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6u_y5f0n/f1.bed /tmp/tmp6u_y5f0n/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqcu27ff7/f1.bed /tmp/tmpqcu27ff7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpad4v62xl/f1.bed /tmp/tmpad4v62xl/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwe32hz1z/f1.bed /tmp/tmpwe32hz1z/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgio2re5g/f1.bed /tmp/tmpgio2re5g/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvnd2dlpb/f1.bed /tmp/tmpvnd2dlpb/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1hokldd1/f1.bed /tmp/tmp1hokldd1/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz441em8k/f1.bed /tmp/tmpz441em8k/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6_s66epb/f1.bed /tmp/tmp6_s66epb/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprz0qumsf/f1.bed /tmp/tmprz0qumsf/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptqvcu504/f1.bed /tmp/tmptqvcu504/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp58ak8jcr/f1.bed /tmp/tmp58ak8jcr/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpm4ksi8rs/f1.bed /tmp/tmpm4ksi8rs/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3m7va8h6/f1.bed /tmp/tmp3m7va8h6/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_ekbtufo/f1.bed /tmp/tmp_ekbtufo/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt6hyq8to/f1.bed /tmp/tmpt6hyq8to/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph3fb65f1/f1.bed /tmp/tmph3fb65f1/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphui7rq1_/f1.bed /tmp/tmphui7rq1_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpftc3cre0/f1.bed /tmp/tmpftc3cre0/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbktahr1f/f1.bed /tmp/tmpbktahr1f/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8vxzc3qi/f1.bed /tmp/tmp8vxzc3qi/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0qo1buas/f1.bed /tmp/tmp0qo1buas/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_lcj05fa/f1.bed /tmp/tmp_lcj05fa/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2x3wqt1k/f1.bed /tmp/tmp2x3wqt1k/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0vbticq_/f1.bed /tmp/tmp0vbticq_/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpof56px1m/f1.bed /tmp/tmpof56px1m/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5fp5zggw/f1.bed /tmp/tmp5fp5zggw/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpm2f9cyzd/f1.bed /tmp/tmpm2f9cyzd/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyoml_i3z/f1.bed /tmp/tmpyoml_i3z/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3c66lti7/f1.bed /tmp/tmp3c66lti7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu_0paxkn/f1.bed /tmp/tmpu_0paxkn/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyiesfmxh/f1.bed /tmp/tmpyiesfmxh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4r94hc6t/f1.bed /tmp/tmp4r94hc6t/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptl6n3hzt/f1.bed /tmp/tmptl6n3hzt/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6jnz01gp/f1.bed /tmp/tmp6jnz01gp/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuofl48in/f1.bed /tmp/tmpuofl48in/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpven3fwna/f1.bed /tmp/tmpven3fwna/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppnb2eetr/f1.bed /tmp/tmppnb2eetr/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmea02ivg/f1.bed /tmp/tmpmea02ivg/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp23hzpoct/f1.bed /tmp/tmp23hzpoct/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9wx7wrhw/f1.bed /tmp/tmp9wx7wrhw/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp91f9cjr2/f1.bed /tmp/tmp91f9cjr2/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmk8nowxh/f1.bed /tmp/tmpmk8nowxh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnuee57yt/f1.bed /tmp/tmpnuee57yt/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppd1y9avf/f1.bed /tmp/tmppd1y9avf/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpchego4fr/f1.bed /tmp/tmpchego4fr/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptmfgptjx/f1.bed /tmp/tmptmfgptjx/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmkmtw445/f1.bed /tmp/tmpmkmtw445/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfjtp3lib/f1.bed /tmp/tmpfjtp3lib/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc5r0rd9u/f1.bed /tmp/tmpc5r0rd9u/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2n7ch8io/f1.bed /tmp/tmp2n7ch8io/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpb2u4wk3x/f1.bed /tmp/tmpb2u4wk3x/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6jaara58/f1.bed /tmp/tmp6jaara58/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp87ey6tmk/f1.bed /tmp/tmp87ey6tmk/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpb1e367yy/f1.bed /tmp/tmpb1e367yy/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzn28j_pb/f1.bed /tmp/tmpzn28j_pb/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcs9prx5x/f1.bed /tmp/tmpcs9prx5x/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________________________ test_subtraction[same] ____________________________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", ["same", "opposite", False]) # tests/test_binary.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:308: in test_subtraction result = gr.subtract(gr2, strandedness=strandedness) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_subtraction( E # The test always failed when commented parts were varied together. E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8hwywrz8/f1.bed -b /tmp/tmp8hwywrz8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmph7uvy28u/f1.bed -b /tmp/tmph7uvy28u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprrhcjlm7/f1.bed -b /tmp/tmprrhcjlm7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpeu5aritf/f1.bed -b /tmp/tmpeu5aritf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmphoa4gba6/f1.bed -b /tmp/tmphoa4gba6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfs4h7qvv/f1.bed -b /tmp/tmpfs4h7qvv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvqegtzsi/f1.bed -b /tmp/tmpvqegtzsi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7rp8nkz8/f1.bed -b /tmp/tmp7rp8nkz8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpz0g0fuiw/f1.bed -b /tmp/tmpz0g0fuiw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpp9kzz4p8/f1.bed -b /tmp/tmpp9kzz4p8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpx7zmuezi/f1.bed -b /tmp/tmpx7zmuezi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpdlz_rf8g/f1.bed -b /tmp/tmpdlz_rf8g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqd7cea6m/f1.bed -b /tmp/tmpqd7cea6m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0ye1do_6/f1.bed -b /tmp/tmp0ye1do_6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmplpoel8kc/f1.bed -b /tmp/tmplpoel8kc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpw9e23rso/f1.bed -b /tmp/tmpw9e23rso/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_gxnsbue/f1.bed -b /tmp/tmp_gxnsbue/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmptf81wxwm/f1.bed -b /tmp/tmptf81wxwm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmaksouw_/f1.bed -b /tmp/tmpmaksouw_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp96jrn_2g/f1.bed -b /tmp/tmp96jrn_2g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpkirm2e9h/f1.bed -b /tmp/tmpkirm2e9h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpz3khwdcq/f1.bed -b /tmp/tmpz3khwdcq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpogw7bqtc/f1.bed -b /tmp/tmpogw7bqtc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfqv5dmmg/f1.bed -b /tmp/tmpfqv5dmmg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzrpvfzpo/f1.bed -b /tmp/tmpzrpvfzpo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpf80t36gb/f1.bed -b /tmp/tmpf80t36gb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwa_qf3om/f1.bed -b /tmp/tmpwa_qf3om/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpe7e3k1ub/f1.bed -b /tmp/tmpe7e3k1ub/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpz9fvrhil/f1.bed -b /tmp/tmpz9fvrhil/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6nge5oqh/f1.bed -b /tmp/tmp6nge5oqh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpc7580bk2/f1.bed -b /tmp/tmpc7580bk2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_z6vecd8/f1.bed -b /tmp/tmp_z6vecd8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfpekpphe/f1.bed -b /tmp/tmpfpekpphe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmplhxxe943/f1.bed -b /tmp/tmplhxxe943/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmphft5328o/f1.bed -b /tmp/tmphft5328o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxa67fuwc/f1.bed -b /tmp/tmpxa67fuwc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpe444cbct/f1.bed -b /tmp/tmpe444cbct/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwl5mxozk/f1.bed -b /tmp/tmpwl5mxozk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgypebwaf/f1.bed -b /tmp/tmpgypebwaf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpntnzlza2/f1.bed -b /tmp/tmpntnzlza2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpla950yep/f1.bed -b /tmp/tmpla950yep/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgrsim7fs/f1.bed -b /tmp/tmpgrsim7fs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpanxm1ct3/f1.bed -b /tmp/tmpanxm1ct3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmam8y2bc/f1.bed -b /tmp/tmpmam8y2bc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpj366u6q4/f1.bed -b /tmp/tmpj366u6q4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvonfaflp/f1.bed -b /tmp/tmpvonfaflp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_mtbo5uy/f1.bed -b /tmp/tmp_mtbo5uy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8ndtexj_/f1.bed -b /tmp/tmp8ndtexj_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqgot8d7j/f1.bed -b /tmp/tmpqgot8d7j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpc_207wnp/f1.bed -b /tmp/tmpc_207wnp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpnk7br6ut/f1.bed -b /tmp/tmpnk7br6ut/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpnmuq51g9/f1.bed -b /tmp/tmpnmuq51g9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqiysk282/f1.bed -b /tmp/tmpqiysk282/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfuyl2v2y/f1.bed -b /tmp/tmpfuyl2v2y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvji8xf07/f1.bed -b /tmp/tmpvji8xf07/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9kl15phx/f1.bed -b /tmp/tmp9kl15phx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpt6yhkx21/f1.bed -b /tmp/tmpt6yhkx21/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp34u381gp/f1.bed -b /tmp/tmp34u381gp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmps42673ts/f1.bed -b /tmp/tmps42673ts/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpkqkpvz8k/f1.bed -b /tmp/tmpkqkpvz8k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1xxt6x9f/f1.bed -b /tmp/tmp1xxt6x9f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbu3q9x4w/f1.bed -b /tmp/tmpbu3q9x4w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpr76r1t29/f1.bed -b /tmp/tmpr76r1t29/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpdvp018ie/f1.bed -b /tmp/tmpdvp018ie/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp16_smg8u/f1.bed -b /tmp/tmp16_smg8u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp16rkybjp/f1.bed -b /tmp/tmp16rkybjp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmptynlyz5s/f1.bed -b /tmp/tmptynlyz5s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwdz2zm3q/f1.bed -b /tmp/tmpwdz2zm3q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8t_ecl63/f1.bed -b /tmp/tmp8t_ecl63/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzxefxgh7/f1.bed -b /tmp/tmpzxefxgh7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2_y_wrml/f1.bed -b /tmp/tmp2_y_wrml/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpb9f_mnpm/f1.bed -b /tmp/tmpb9f_mnpm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqhfbdqhn/f1.bed -b /tmp/tmpqhfbdqhn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpoi093qhr/f1.bed -b /tmp/tmpoi093qhr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpshfyrgnq/f1.bed -b /tmp/tmpshfyrgnq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpnn19h9fj/f1.bed -b /tmp/tmpnn19h9fj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfx0nrqrg/f1.bed -b /tmp/tmpfx0nrqrg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmzqe7ymq/f1.bed -b /tmp/tmpmzqe7ymq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpcjgq6xjk/f1.bed -b /tmp/tmpcjgq6xjk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpokfvmxvy/f1.bed -b /tmp/tmpokfvmxvy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzpw38016/f1.bed -b /tmp/tmpzpw38016/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpc52t3g77/f1.bed -b /tmp/tmpc52t3g77/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqcrqfiia/f1.bed -b /tmp/tmpqcrqfiia/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpows2rax5/f1.bed -b /tmp/tmpows2rax5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzcszffwx/f1.bed -b /tmp/tmpzcszffwx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9iiloyq6/f1.bed -b /tmp/tmp9iiloyq6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpz3jfasbw/f1.bed -b /tmp/tmpz3jfasbw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfmsggjxq/f1.bed -b /tmp/tmpfmsggjxq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjzj_sok7/f1.bed -b /tmp/tmpjzj_sok7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmptegxk72v/f1.bed -b /tmp/tmptegxk72v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp724f33f3/f1.bed -b /tmp/tmp724f33f3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpd76nnc83/f1.bed -b /tmp/tmpd76nnc83/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp43_zqzsi/f1.bed -b /tmp/tmp43_zqzsi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7dz6xk7o/f1.bed -b /tmp/tmp7dz6xk7o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmphyspwtel/f1.bed -b /tmp/tmphyspwtel/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpt4of7osn/f1.bed -b /tmp/tmpt4of7osn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxkfpjcuy/f1.bed -b /tmp/tmpxkfpjcuy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmph1nnmc_m/f1.bed -b /tmp/tmph1nnmc_m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmphbcc23wj/f1.bed -b /tmp/tmphbcc23wj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxlefl81q/f1.bed -b /tmp/tmpxlefl81q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvuzga_um/f1.bed -b /tmp/tmpvuzga_um/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmwfwth1s/f1.bed -b /tmp/tmpmwfwth1s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpx882rmma/f1.bed -b /tmp/tmpx882rmma/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5gpoh9mx/f1.bed -b /tmp/tmp5gpoh9mx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5d3juz33/f1.bed -b /tmp/tmp5d3juz33/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpg47daw4a/f1.bed -b /tmp/tmpg47daw4a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmcjykn_p/f1.bed -b /tmp/tmpmcjykn_p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpw6beztx0/f1.bed -b /tmp/tmpw6beztx0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpilxgayug/f1.bed -b /tmp/tmpilxgayug/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1x218o8u/f1.bed -b /tmp/tmp1x218o8u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqbv9twrn/f1.bed -b /tmp/tmpqbv9twrn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmrl9cpuj/f1.bed -b /tmp/tmpmrl9cpuj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0ed9czwl/f1.bed -b /tmp/tmp0ed9czwl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpkre01c68/f1.bed -b /tmp/tmpkre01c68/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8yzinyuc/f1.bed -b /tmp/tmp8yzinyuc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpy415im_x/f1.bed -b /tmp/tmpy415im_x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxsy1dmm8/f1.bed -b /tmp/tmpxsy1dmm8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp68l4sbgw/f1.bed -b /tmp/tmp68l4sbgw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwva5u46v/f1.bed -b /tmp/tmpwva5u46v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmoy3oxvl/f1.bed -b /tmp/tmpmoy3oxvl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8ftq3e3f/f1.bed -b /tmp/tmp8ftq3e3f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp79ubvb1o/f1.bed -b /tmp/tmp79ubvb1o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpydm86d_m/f1.bed -b /tmp/tmpydm86d_m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpw5v_qtd6/f1.bed -b /tmp/tmpw5v_qtd6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfqelafwf/f1.bed -b /tmp/tmpfqelafwf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqrh8pc4j/f1.bed -b /tmp/tmpqrh8pc4j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpa5507y_9/f1.bed -b /tmp/tmpa5507y_9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmppl3kvm2m/f1.bed -b /tmp/tmppl3kvm2m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9re8sg9m/f1.bed -b /tmp/tmp9re8sg9m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp24q0x3jx/f1.bed -b /tmp/tmp24q0x3jx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp55w4c1s5/f1.bed -b /tmp/tmp55w4c1s5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp454zo46_/f1.bed -b /tmp/tmp454zo46_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpsys4iupp/f1.bed -b /tmp/tmpsys4iupp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxacwqnrv/f1.bed -b /tmp/tmpxacwqnrv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp14gkeajw/f1.bed -b /tmp/tmp14gkeajw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp39s3buvi/f1.bed -b /tmp/tmp39s3buvi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3gronu8y/f1.bed -b /tmp/tmp3gronu8y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpd7s0h5kt/f1.bed -b /tmp/tmpd7s0h5kt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7u3qezg0/f1.bed -b /tmp/tmp7u3qezg0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpz7cuh6_e/f1.bed -b /tmp/tmpz7cuh6_e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpez7geuk5/f1.bed -b /tmp/tmpez7geuk5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpduepqikk/f1.bed -b /tmp/tmpduepqikk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4l0e6c1m/f1.bed -b /tmp/tmp4l0e6c1m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwu4m99n7/f1.bed -b /tmp/tmpwu4m99n7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpdpwynvy0/f1.bed -b /tmp/tmpdpwynvy0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpazwdegrw/f1.bed -b /tmp/tmpazwdegrw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmppcm25yb8/f1.bed -b /tmp/tmppcm25yb8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpck7xxdo3/f1.bed -b /tmp/tmpck7xxdo3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2jmtqf4u/f1.bed -b /tmp/tmp2jmtqf4u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpkp8061ms/f1.bed -b /tmp/tmpkp8061ms/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmqr_yp7x/f1.bed -b /tmp/tmpmqr_yp7x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqevbqxyf/f1.bed -b /tmp/tmpqevbqxyf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7aar7tdl/f1.bed -b /tmp/tmp7aar7tdl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbofkyw3i/f1.bed -b /tmp/tmpbofkyw3i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpusnv6pq2/f1.bed -b /tmp/tmpusnv6pq2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpl2698ud3/f1.bed -b /tmp/tmpl2698ud3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbqx3i3sj/f1.bed -b /tmp/tmpbqx3i3sj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgmlx5z0e/f1.bed -b /tmp/tmpgmlx5z0e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxfexbrtt/f1.bed -b /tmp/tmpxfexbrtt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2hx8hrl3/f1.bed -b /tmp/tmp2hx8hrl3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_f9ndl17/f1.bed -b /tmp/tmp_f9ndl17/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5ru8ri15/f1.bed -b /tmp/tmp5ru8ri15/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpx17f9iqw/f1.bed -b /tmp/tmpx17f9iqw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpk5y84k3i/f1.bed -b /tmp/tmpk5y84k3i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpb4du3206/f1.bed -b /tmp/tmpb4du3206/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpx0jqe2zd/f1.bed -b /tmp/tmpx0jqe2zd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6mzps2qr/f1.bed -b /tmp/tmp6mzps2qr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpolmdo0s5/f1.bed -b /tmp/tmpolmdo0s5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpm2i_zl89/f1.bed -b /tmp/tmpm2i_zl89/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpulazmota/f1.bed -b /tmp/tmpulazmota/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpy24hanc3/f1.bed -b /tmp/tmpy24hanc3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9n36wdzf/f1.bed -b /tmp/tmp9n36wdzf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpg7cut1r9/f1.bed -b /tmp/tmpg7cut1r9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpd_0tdzvm/f1.bed -b /tmp/tmpd_0tdzvm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvj1acpdf/f1.bed -b /tmp/tmpvj1acpdf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpoq83jfrp/f1.bed -b /tmp/tmpoq83jfrp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3c5wyfgk/f1.bed -b /tmp/tmp3c5wyfgk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4h11uuas/f1.bed -b /tmp/tmp4h11uuas/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpnu1ujh7h/f1.bed -b /tmp/tmpnu1ujh7h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpsxhim_jk/f1.bed -b /tmp/tmpsxhim_jk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp79hprr1k/f1.bed -b /tmp/tmp79hprr1k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_89bloaa/f1.bed -b /tmp/tmp_89bloaa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqeq6s1_t/f1.bed -b /tmp/tmpqeq6s1_t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpdjjjnpdy/f1.bed -b /tmp/tmpdjjjnpdy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpffoc1isd/f1.bed -b /tmp/tmpffoc1isd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp51deg1er/f1.bed -b /tmp/tmp51deg1er/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1s2g7v27/f1.bed -b /tmp/tmp1s2g7v27/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpdbw7rzne/f1.bed -b /tmp/tmpdbw7rzne/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9a8mp4s3/f1.bed -b /tmp/tmp9a8mp4s3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp08xqdgxy/f1.bed -b /tmp/tmp08xqdgxy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpkhcyr6mk/f1.bed -b /tmp/tmpkhcyr6mk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqg4vbn76/f1.bed -b /tmp/tmpqg4vbn76/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3tz86vd8/f1.bed -b /tmp/tmp3tz86vd8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpeskj2zhv/f1.bed -b /tmp/tmpeskj2zhv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprc2ljry9/f1.bed -b /tmp/tmprc2ljry9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpyw6mutnm/f1.bed -b /tmp/tmpyw6mutnm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmh11bx31/f1.bed -b /tmp/tmpmh11bx31/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpegorqqgc/f1.bed -b /tmp/tmpegorqqgc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpw6mkqgqc/f1.bed -b /tmp/tmpw6mkqgqc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0q3dd3dk/f1.bed -b /tmp/tmp0q3dd3dk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpqobho2oi/f1.bed -b /tmp/tmpqobho2oi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxlf82sjc/f1.bed -b /tmp/tmpxlf82sjc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4kmfimqn/f1.bed -b /tmp/tmp4kmfimqn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpsw_zn4km/f1.bed -b /tmp/tmpsw_zn4km/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpkrbv3x2h/f1.bed -b /tmp/tmpkrbv3x2h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4s5potp_/f1.bed -b /tmp/tmp4s5potp_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpnl20icbp/f1.bed -b /tmp/tmpnl20icbp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpkuuallme/f1.bed -b /tmp/tmpkuuallme/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmxclqigm/f1.bed -b /tmp/tmpmxclqigm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzbm0prxb/f1.bed -b /tmp/tmpzbm0prxb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp34smqidu/f1.bed -b /tmp/tmp34smqidu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9d19g8ox/f1.bed -b /tmp/tmp9d19g8ox/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpj2sx5cmn/f1.bed -b /tmp/tmpj2sx5cmn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6tz63wj1/f1.bed -b /tmp/tmp6tz63wj1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp959ga5gi/f1.bed -b /tmp/tmp959ga5gi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp27meom1o/f1.bed -b /tmp/tmp27meom1o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpa72u36tz/f1.bed -b /tmp/tmpa72u36tz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9brfb3b4/f1.bed -b /tmp/tmp9brfb3b4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7v62oove/f1.bed -b /tmp/tmp7v62oove/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxaswrjf2/f1.bed -b /tmp/tmpxaswrjf2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjpvh2ib2/f1.bed -b /tmp/tmpjpvh2ib2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6x0_9mzy/f1.bed -b /tmp/tmp6x0_9mzy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpyn4xeshu/f1.bed -b /tmp/tmpyn4xeshu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpv4oyz77s/f1.bed -b /tmp/tmpv4oyz77s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0e08hvw5/f1.bed -b /tmp/tmp0e08hvw5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprpcmpt5h/f1.bed -b /tmp/tmprpcmpt5h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpr250n724/f1.bed -b /tmp/tmpr250n724/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmplnihlj85/f1.bed -b /tmp/tmplnihlj85/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpazvd4bac/f1.bed -b /tmp/tmpazvd4bac/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmptqf_g1ap/f1.bed -b /tmp/tmptqf_g1ap/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpatw66gnb/f1.bed -b /tmp/tmpatw66gnb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpsotxyuc8/f1.bed -b /tmp/tmpsotxyuc8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpnh6jiv6b/f1.bed -b /tmp/tmpnh6jiv6b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbkxq_uwb/f1.bed -b /tmp/tmpbkxq_uwb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpamq0ed0u/f1.bed -b /tmp/tmpamq0ed0u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpurp02erk/f1.bed -b /tmp/tmpurp02erk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbn97kgc7/f1.bed -b /tmp/tmpbn97kgc7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmuj8impx/f1.bed -b /tmp/tmpmuj8impx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6x6lvege/f1.bed -b /tmp/tmp6x6lvege/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6618qnd7/f1.bed -b /tmp/tmp6618qnd7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfugx5sq3/f1.bed -b /tmp/tmpfugx5sq3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3hbpolhg/f1.bed -b /tmp/tmp3hbpolhg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjyu748u_/f1.bed -b /tmp/tmpjyu748u_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp55sga_uv/f1.bed -b /tmp/tmp55sga_uv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpe7dtv9ld/f1.bed -b /tmp/tmpe7dtv9ld/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpoi7n425f/f1.bed -b /tmp/tmpoi7n425f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpb1hk6j0w/f1.bed -b /tmp/tmpb1hk6j0w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpkbeadenn/f1.bed -b /tmp/tmpkbeadenn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpocnto3i7/f1.bed -b /tmp/tmpocnto3i7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6brev9pp/f1.bed -b /tmp/tmp6brev9pp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpncp00czj/f1.bed -b /tmp/tmpncp00czj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7rjroqs3/f1.bed -b /tmp/tmp7rjroqs3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpp9wf4aev/f1.bed -b /tmp/tmpp9wf4aev/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp6ls1om7o/f1.bed -b /tmp/tmp6ls1om7o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpd_0kunxz/f1.bed -b /tmp/tmpd_0kunxz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpn775rr2q/f1.bed -b /tmp/tmpn775rr2q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmplz0pzu7b/f1.bed -b /tmp/tmplz0pzu7b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmprfmg8acq/f1.bed -b /tmp/tmprfmg8acq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp202k593w/f1.bed -b /tmp/tmp202k593w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmplovgwa3p/f1.bed -b /tmp/tmplovgwa3p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_pe6fwyt/f1.bed -b /tmp/tmp_pe6fwyt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp257p3mgx/f1.bed -b /tmp/tmp257p3mgx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpeivtfx15/f1.bed -b /tmp/tmpeivtfx15/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpeiegm7yj/f1.bed -b /tmp/tmpeiegm7yj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpyproyhvr/f1.bed -b /tmp/tmpyproyhvr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmph1o_l2mz/f1.bed -b /tmp/tmph1o_l2mz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpshni9i8j/f1.bed -b /tmp/tmpshni9i8j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmptzyk7qc1/f1.bed -b /tmp/tmptzyk7qc1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgs_c0bzh/f1.bed -b /tmp/tmpgs_c0bzh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpyd63808o/f1.bed -b /tmp/tmpyd63808o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpme5v11p6/f1.bed -b /tmp/tmpme5v11p6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxuy6tvvb/f1.bed -b /tmp/tmpxuy6tvvb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7gt00l16/f1.bed -b /tmp/tmp7gt00l16/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3kmo3u17/f1.bed -b /tmp/tmp3kmo3u17/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfz1yivbj/f1.bed -b /tmp/tmpfz1yivbj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpk1i2o7ua/f1.bed -b /tmp/tmpk1i2o7ua/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8awc5eln/f1.bed -b /tmp/tmp8awc5eln/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpa35u75sl/f1.bed -b /tmp/tmpa35u75sl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp32zir06n/f1.bed -b /tmp/tmp32zir06n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpe1qep825/f1.bed -b /tmp/tmpe1qep825/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp81ysuwmo/f1.bed -b /tmp/tmp81ysuwmo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpp32ix8ar/f1.bed -b /tmp/tmpp32ix8ar/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgmjw3sux/f1.bed -b /tmp/tmpgmjw3sux/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp38lk2zjs/f1.bed -b /tmp/tmp38lk2zjs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp366wp0no/f1.bed -b /tmp/tmp366wp0no/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp0d6h_pj4/f1.bed -b /tmp/tmp0d6h_pj4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvp3x6y5l/f1.bed -b /tmp/tmpvp3x6y5l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4wq23qdr/f1.bed -b /tmp/tmp4wq23qdr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfwxdq2pq/f1.bed -b /tmp/tmpfwxdq2pq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpoxkgfwsx/f1.bed -b /tmp/tmpoxkgfwsx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpv0cgi7pb/f1.bed -b /tmp/tmpv0cgi7pb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpiayrg5bz/f1.bed -b /tmp/tmpiayrg5bz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwxilmtt3/f1.bed -b /tmp/tmpwxilmtt3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfne9wnxx/f1.bed -b /tmp/tmpfne9wnxx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2mng3ge3/f1.bed -b /tmp/tmp2mng3ge3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpk_exm3o5/f1.bed -b /tmp/tmpk_exm3o5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpj3fxytw9/f1.bed -b /tmp/tmpj3fxytw9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpu1m0hqzs/f1.bed -b /tmp/tmpu1m0hqzs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpecfxyuz4/f1.bed -b /tmp/tmpecfxyuz4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9wdxdibl/f1.bed -b /tmp/tmp9wdxdibl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpa4r7ncbw/f1.bed -b /tmp/tmpa4r7ncbw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmppi5gn9k1/f1.bed -b /tmp/tmppi5gn9k1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp03_txs57/f1.bed -b /tmp/tmp03_txs57/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpy8nhr08n/f1.bed -b /tmp/tmpy8nhr08n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp71mrry_v/f1.bed -b /tmp/tmp71mrry_v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmppmm5bxlb/f1.bed -b /tmp/tmppmm5bxlb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5suywqln/f1.bed -b /tmp/tmp5suywqln/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwxdnx7hl/f1.bed -b /tmp/tmpwxdnx7hl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxwtmiua0/f1.bed -b /tmp/tmpxwtmiua0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwr5jgdps/f1.bed -b /tmp/tmpwr5jgdps/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpok186850/f1.bed -b /tmp/tmpok186850/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmphsk3xn16/f1.bed -b /tmp/tmphsk3xn16/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4oclwqox/f1.bed -b /tmp/tmp4oclwqox/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpx0w_41gh/f1.bed -b /tmp/tmpx0w_41gh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpwqt4cjli/f1.bed -b /tmp/tmpwqt4cjli/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpr72vua4q/f1.bed -b /tmp/tmpr72vua4q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpjv200ga2/f1.bed -b /tmp/tmpjv200ga2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpc6ptnvor/f1.bed -b /tmp/tmpc6ptnvor/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpynwnluvj/f1.bed -b /tmp/tmpynwnluvj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpv99gcm6r/f1.bed -b /tmp/tmpv99gcm6r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpuh31qnq1/f1.bed -b /tmp/tmpuh31qnq1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpc5tbdj1y/f1.bed -b /tmp/tmpc5tbdj1y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmplhmv_vuy/f1.bed -b /tmp/tmplhmv_vuy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpier3u3op/f1.bed -b /tmp/tmpier3u3op/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpq78g56_9/f1.bed -b /tmp/tmpq78g56_9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpoxa3y0nv/f1.bed -b /tmp/tmpoxa3y0nv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpo26d90fz/f1.bed -b /tmp/tmpo26d90fz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9vzfcphx/f1.bed -b /tmp/tmp9vzfcphx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgws37z7u/f1.bed -b /tmp/tmpgws37z7u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbuve3ruz/f1.bed -b /tmp/tmpbuve3ruz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpde49n5ad/f1.bed -b /tmp/tmpde49n5ad/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgf95mb8p/f1.bed -b /tmp/tmpgf95mb8p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgydyd6ul/f1.bed -b /tmp/tmpgydyd6ul/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpg_dxak3i/f1.bed -b /tmp/tmpg_dxak3i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfsar8j3s/f1.bed -b /tmp/tmpfsar8j3s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbq44ifbb/f1.bed -b /tmp/tmpbq44ifbb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvqwacjq9/f1.bed -b /tmp/tmpvqwacjq9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpghcowqq9/f1.bed -b /tmp/tmpghcowqq9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2dl_t0og/f1.bed -b /tmp/tmp2dl_t0og/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpp8s5xx3i/f1.bed -b /tmp/tmpp8s5xx3i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfwtftoe9/f1.bed -b /tmp/tmpfwtftoe9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmparj17xho/f1.bed -b /tmp/tmparj17xho/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpq5pf62lr/f1.bed -b /tmp/tmpq5pf62lr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpybg_spa4/f1.bed -b /tmp/tmpybg_spa4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1q17b69t/f1.bed -b /tmp/tmp1q17b69t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvepu7tu6/f1.bed -b /tmp/tmpvepu7tu6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmppglydj77/f1.bed -b /tmp/tmppglydj77/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpq_tczhfn/f1.bed -b /tmp/tmpq_tczhfn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp03orbe5v/f1.bed -b /tmp/tmp03orbe5v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpeaihgv_2/f1.bed -b /tmp/tmpeaihgv_2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpscr09x7s/f1.bed -b /tmp/tmpscr09x7s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpuaxeq8ht/f1.bed -b /tmp/tmpuaxeq8ht/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpss3afi9h/f1.bed -b /tmp/tmpss3afi9h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmps9ukxcok/f1.bed -b /tmp/tmps9ukxcok/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpapiv0n2t/f1.bed -b /tmp/tmpapiv0n2t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmplgtnyb3o/f1.bed -b /tmp/tmplgtnyb3o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpmhyff4vz/f1.bed -b /tmp/tmpmhyff4vz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpbhiud1k5/f1.bed -b /tmp/tmpbhiud1k5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2d1pz51k/f1.bed -b /tmp/tmp2d1pz51k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpz3f99es3/f1.bed -b /tmp/tmpz3f99es3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2bym2zm4/f1.bed -b /tmp/tmp2bym2zm4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9y0op73e/f1.bed -b /tmp/tmp9y0op73e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpfx404mvw/f1.bed -b /tmp/tmpfx404mvw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpc527em_h/f1.bed -b /tmp/tmpc527em_h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp5q03fuaf/f1.bed -b /tmp/tmp5q03fuaf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpv2o7ch3i/f1.bed -b /tmp/tmpv2o7ch3i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp2ftiv3qi/f1.bed -b /tmp/tmp2ftiv3qi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpg9pwzw62/f1.bed -b /tmp/tmpg9pwzw62/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpy9drtfn0/f1.bed -b /tmp/tmpy9drtfn0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8762ngof/f1.bed -b /tmp/tmp8762ngof/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpb5pioo89/f1.bed -b /tmp/tmpb5pioo89/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpr7gwfzm5/f1.bed -b /tmp/tmpr7gwfzm5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp86gmgo0y/f1.bed -b /tmp/tmp86gmgo0y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpd_1w3d1t/f1.bed -b /tmp/tmpd_1w3d1t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp12vleu7y/f1.bed -b /tmp/tmp12vleu7y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpgtsv3z4c/f1.bed -b /tmp/tmpgtsv3z4c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpq5ftsw4x/f1.bed -b /tmp/tmpq5ftsw4x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzg5dt8a2/f1.bed -b /tmp/tmpzg5dt8a2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpsi7xm3tc/f1.bed -b /tmp/tmpsi7xm3tc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9czwat6u/f1.bed -b /tmp/tmp9czwat6u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp89x4vusg/f1.bed -b /tmp/tmp89x4vusg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4k0i0h5_/f1.bed -b /tmp/tmp4k0i0h5_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmps8y46npe/f1.bed -b /tmp/tmps8y46npe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpk4scl2jy/f1.bed -b /tmp/tmpk4scl2jy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9opcmaki/f1.bed -b /tmp/tmp9opcmaki/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpi461hkdh/f1.bed -b /tmp/tmpi461hkdh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxdbugeub/f1.bed -b /tmp/tmpxdbugeub/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpv3qiylf8/f1.bed -b /tmp/tmpv3qiylf8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpaa6a3h4b/f1.bed -b /tmp/tmpaa6a3h4b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpdtop3am0/f1.bed -b /tmp/tmpdtop3am0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp09i_iv7h/f1.bed -b /tmp/tmp09i_iv7h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpkbabe6sn/f1.bed -b /tmp/tmpkbabe6sn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzp0oxiu9/f1.bed -b /tmp/tmpzp0oxiu9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp_dc2f9sd/f1.bed -b /tmp/tmp_dc2f9sd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpc6b3g8rm/f1.bed -b /tmp/tmpc6b3g8rm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzkoiff87/f1.bed -b /tmp/tmpzkoiff87/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvt29b085/f1.bed -b /tmp/tmpvt29b085/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpdf_6bpaa/f1.bed -b /tmp/tmpdf_6bpaa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpaovkmap3/f1.bed -b /tmp/tmpaovkmap3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpy7ht_gyz/f1.bed -b /tmp/tmpy7ht_gyz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8fq0y9fd/f1.bed -b /tmp/tmp8fq0y9fd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmph58brzed/f1.bed -b /tmp/tmph58brzed/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp9e0q5smi/f1.bed -b /tmp/tmp9e0q5smi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpg43xty_u/f1.bed -b /tmp/tmpg43xty_u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpl7okb4wj/f1.bed -b /tmp/tmpl7okb4wj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpckhfwfvi/f1.bed -b /tmp/tmpckhfwfvi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8uac5zca/f1.bed -b /tmp/tmp8uac5zca/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpk4fqng4f/f1.bed -b /tmp/tmpk4fqng4f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp34upcta1/f1.bed -b /tmp/tmp34upcta1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp33b0rqxp/f1.bed -b /tmp/tmp33b0rqxp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpj0zbnzcm/f1.bed -b /tmp/tmpj0zbnzcm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpke75jvyn/f1.bed -b /tmp/tmpke75jvyn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp60i_3xmf/f1.bed -b /tmp/tmp60i_3xmf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpsn026cqb/f1.bed -b /tmp/tmpsn026cqb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting ___________ test_three_in_a_row[strandedness_chain68-method_chain68] ___________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ___________ test_three_in_a_row[strandedness_chain39-method_chain39] ___________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ___________ test_three_in_a_row[strandedness_chain62-method_chain62] ___________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E /usr/lib/python3/dist-packages/pandas/core/common.py:143 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ___________ test_three_in_a_row[strandedness_chain53-method_chain53] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 178 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') _____________________ test_k_nearest[None-True-False-last] _____________________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 nearest_how = None, overlap = True, strandedness = False, ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=True, E strandedness=False, E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:19 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:28 E (and 36 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:28: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3dwyflp8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3dwyflp8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmprav5xms7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprav5xms7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4uynfgt2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4uynfgt2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxhuzl7xa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxhuzl7xa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptupgi85y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptupgi85y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfuql000j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfuql000j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8vj4d__d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8vj4d__d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1_fi9w5s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1_fi9w5s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1w_t90jw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1w_t90jw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpokw5mcw4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpokw5mcw4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnjuz6lkh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnjuz6lkh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj_95dk15/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj_95dk15/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6ulxkj9b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ulxkj9b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvrnn_o1f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvrnn_o1f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp21maw41l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp21maw41l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6_ve61_t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6_ve61_t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_pk94tpb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_pk94tpb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3xik_n4n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3xik_n4n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbrn629w7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbrn629w7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkktxktk8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkktxktk8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmph8itfg2e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph8itfg2e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphds6f0_4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphds6f0_4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu722j6fz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu722j6fz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeirlei6n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeirlei6n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3agm66v1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3agm66v1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfn3gbnd3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfn3gbnd3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2mbm7oaw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2mbm7oaw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpajqngrdt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpajqngrdt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn8taw9vb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn8taw9vb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpje4s5tx9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpje4s5tx9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp48g7a_lz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp48g7a_lz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpudcatvmx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpudcatvmx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiezr75vz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiezr75vz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyskq95g6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyskq95g6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplajsg92r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplajsg92r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiqh_64bp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiqh_64bp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp12t8ltp3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp12t8ltp3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkni12vf2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkni12vf2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkx03smv8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkx03smv8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpszjyky32/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpszjyky32/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplvukeipx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplvukeipx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe8h0637r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8h0637r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsycw6gjh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsycw6gjh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfchktey5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfchktey5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9wzam10z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9wzam10z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_jfwmvt9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_jfwmvt9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcpastpzp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcpastpzp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptfuqp2u3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptfuqp2u3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpouvb6z31/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpouvb6z31/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_ugc728_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ugc728_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp84q1thm2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp84q1thm2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpldlirbgi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpldlirbgi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3zuujc64/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3zuujc64/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5ofksx2l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ofksx2l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwp1hahy8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwp1hahy8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8zztutl6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8zztutl6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbbjdwmxl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbbjdwmxl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu3a24h_w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu3a24h_w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr485nfr6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr485nfr6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1lt477v0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1lt477v0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx_enly76/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx_enly76/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpov95dxns/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpov95dxns/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr16 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain40-method_chain40] ___________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2691953 | 2691954 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2691953 | 2691954 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2691953 | 2691954 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2691953 | 2691954 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2691953 | 2691954 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2691953 | 2691954 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ___________ test_three_in_a_row[strandedness_chain63-method_chain63] ___________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:21 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:37 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:43 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ___________ test_three_in_a_row[strandedness_chain54-method_chain54] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E /usr/lib/python3/dist-packages/natsort/utils.py:500 E (and 117 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ___________ test_three_in_a_row[strandedness_chain14-method_chain14] ___________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:21 E (and 141 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges 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______________________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.End) | ^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 3086 | 3087 | a | 0 | - | | | chr1 | 3086 | 3087 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | (and 65 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RWN/dldGRkYHAEQgYnHj5GIIMRgiDijDDEAABvawRj') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.Start, ocdf.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_ends.values - 1, right_starts.values, right_indexes) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | (and 64 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGRyYGINuRgREswghDDAAx2gLW') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | ~~~~~~~~~~~~~~~~~~~^ | lcol, | ^^^^^ | ...<12 lines>... | check_flags=False, | ^^^^^^^^^^^^^^^^^^ | ) | ^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/init.py:174 | (and 454 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3Rh6LwQxcDgyAhDDIxAEpkPAF/lBEo=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc0nu7p12/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc0nu7p12/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp97puum3j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp97puum3j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9m8msbst/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9m8msbst/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1506744 1516623 + 0 1 chr1 3420281 3420549 + 0 2 chr1 7265147 7265225 - 0 3 chr1 9340904 9341172 - 0 4 chr14 1947346 1955026 + 0 5 chr22 8381603 8381871 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3420281 | 3420549 | a | 0 | ... | | chr1 | 1506744 | 1516623 | a | 0 | ... | | chr1 | 9340904 | 9341172 | a | 0 | ... | | chr1 | 7265147 | 7265225 | a | 0 | ... | | chr14 | 1947346 | 1955026 | a | 0 | ... | | chr22 | 8381603 | 8381871 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1506744 1516623 + 0 4 chr14 1947346 1955026 + 0 0 chr1 3420281 3420549 + 0 3 chr1 7265147 7265225 - 0 5 chr22 8381603 8381871 + 0 2 chr1 9340904 9341172 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1506744 1516623 + 0 4 chr14 1947346 1955026 + 0 1 chr1 3420281 3420549 + 0 2 chr1 7265147 7265225 - 0 5 chr22 8381603 8381871 + 0 3 chr1 9340904 9341172 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1506744 1516623 + 0 1 chr1 3420281 3420549 + 0 2 chr1 7265147 7265225 - 0 3 chr1 9340904 9341172 - 0 4 chr14 1947346 1955026 + 0 5 chr22 8381603 8381871 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1506744 1516623 + 0 1 chr1 3420281 3420549 + 0 2 chr1 7265147 7265225 - 0 3 chr1 9340904 9341172 - 0 4 chr14 1947346 1955026 + 0 5 chr22 8381603 8381871 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz3mejzvj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz3mejzvj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprk522zd7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprk522zd7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1506744 1516623 + 0 1 chr1 3420281 3420549 + 0 2 chr1 7265147 7265225 - 0 3 chr1 9340904 9341172 - 0 4 chr14 1947346 1955026 + 0 5 chr22 8381603 8381871 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3420281 | 3420549 | a | 0 | ... | | chr1 | 1506744 | 1516623 | a | 0 | ... | | chr1 | 9340904 | 9341172 | a | 0 | ... | | chr1 | 7265147 | 7265225 | a | 0 | ... | | chr14 | 1947346 | 1955026 | a | 0 | ... | | chr22 | 8381603 | 8381871 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1506744 1516623 + 0 4 chr14 1947346 1955026 + 0 0 chr1 3420281 3420549 + 0 3 chr1 7265147 7265225 - 0 5 chr22 8381603 8381871 + 0 2 chr1 9340904 9341172 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1506744 1516623 + 0 4 chr14 1947346 1955026 + 0 1 chr1 3420281 3420549 + 0 2 chr1 7265147 7265225 - 0 5 chr22 8381603 8381871 + 0 3 chr1 9340904 9341172 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1506744 1516623 + 0 1 chr1 3420281 3420549 + 0 2 chr1 7265147 7265225 - 0 3 chr1 9340904 9341172 - 0 4 chr14 1947346 1955026 + 0 5 chr22 8381603 8381871 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1506744 1516623 + 0 1 chr1 3420281 3420549 + 0 2 chr1 7265147 7265225 - 0 3 chr1 9340904 9341172 - 0 4 chr14 1947346 1955026 + 0 5 chr22 8381603 8381871 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk4uzyeu4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk4uzyeu4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7_p4qud5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7_p4qud5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1506744 1516623 + 0 1 chr1 3420281 3420549 + 0 2 chr1 7265147 7265225 - 0 3 chr1 9340904 9341172 - 0 4 chr14 1947346 1955026 + 0 5 chr22 8381603 8381871 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3420281 | 3420549 | a | 0 | ... | | chr1 | 1506744 | 1516623 | a | 0 | ... | | chr1 | 9340904 | 9341172 | a | 0 | ... | | chr1 | 7265147 | 7265225 | a | 0 | ... | | chr14 | 1947346 | 1955026 | a | 0 | ... | | chr22 | 8381603 | 8381871 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1506744 1516623 + 0 4 chr14 1947346 1955026 + 0 0 chr1 3420281 3420549 + 0 3 chr1 7265147 7265225 - 0 5 chr22 8381603 8381871 + 0 2 chr1 9340904 9341172 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1506744 1516623 + 0 4 chr14 1947346 1955026 + 0 1 chr1 3420281 3420549 + 0 2 chr1 7265147 7265225 - 0 5 chr22 8381603 8381871 + 0 3 chr1 9340904 9341172 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1506744 1516623 + 0 1 chr1 3420281 3420549 + 0 2 chr1 7265147 7265225 - 0 3 chr1 9340904 9341172 - 0 4 chr14 1947346 1955026 + 0 5 chr22 8381603 8381871 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1506744 1516623 + 0 1 chr1 3420281 3420549 + 0 2 chr1 7265147 7265225 - 0 3 chr1 9340904 9341172 - 0 4 chr14 1947346 1955026 + 0 5 chr22 8381603 8381871 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp08ub11nx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp08ub11nx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph1rr7zbu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph1rr7zbu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb5xm864f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb5xm864f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf_k7e95l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf_k7e95l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2qwgp9ez/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2qwgp9ez/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk6m0iode/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk6m0iode/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpto9pmgmf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpto9pmgmf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp12rk_7ws/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp12rk_7ws/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5ffeu3bf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ffeu3bf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo0vf_6_c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo0vf_6_c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppbefeprq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppbefeprq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyj27xezo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyj27xezo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5qozkehg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5qozkehg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw6bac4fp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw6bac4fp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_sn6levq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_sn6levq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprff9iugo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprff9iugo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppq9qa_ta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppq9qa_ta/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc1jw9ad3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc1jw9ad3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptuypx6xp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptuypx6xp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_eg2qrll/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_eg2qrll/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgpo2jvt3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgpo2jvt3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp23xlhiw7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp23xlhiw7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1wkomcqr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1wkomcqr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0fibo28x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0fibo28x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfliz4c_m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfliz4c_m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7vrijcnv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7vrijcnv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdc9zkjar/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdc9zkjar/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgsmg2vo7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgsmg2vo7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl_g35dhy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl_g35dhy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6pt1zss1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6pt1zss1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp56l4vyxq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp56l4vyxq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjn0y7nex/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjn0y7nex/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaouxy7lk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaouxy7lk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmuziaaox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmuziaaox/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1yshykrf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1yshykrf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf2wbtvl4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf2wbtvl4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpecvoi3ic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpecvoi3ic/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7oolpwd3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7oolpwd3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5mr0em8b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5mr0em8b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptaqi3bsm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptaqi3bsm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn1bxsoig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn1bxsoig/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptlctdwns/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptlctdwns/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpssbwdbsa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpssbwdbsa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphjzh9_74/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphjzh9_74/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprrpczez2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprrpczez2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9qykug6j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qykug6j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0_sgs4pb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_sgs4pb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp36aq89o5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36aq89o5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwxbag305/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwxbag305/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_vujzk9t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_vujzk9t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph3kdbyhq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph3kdbyhq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoyomu_9k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoyomu_9k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzmrtseq9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzmrtseq9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4x3dk16d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4x3dk16d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk7dpfxp6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk7dpfxp6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5yyo35kk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5yyo35kk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcbdbydz1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcbdbydz1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprp12j2je/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprp12j2je/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9xwlpa0p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9xwlpa0p/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnz7g_3t8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnz7g_3t8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps1odswbp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps1odswbp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwwr2fmrr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwwr2fmrr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzybxk4_5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzybxk4_5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb6kb9j5n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb6kb9j5n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx3mdoyn_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3mdoyn_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy3bm3swg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy3bm3swg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm0cmf58s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm0cmf58s/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaaqj4i7t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaaqj4i7t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpft0w__4y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpft0w__4y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzrek8fww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzrek8fww/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4818 4819 + 0 1 chr1 4818 4819 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4818 | 4819 | a | 0 | ... | | chr1 | 4818 | 4819 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4818 4819 + 0 1 chr1 4818 4819 - 0 df2 Chromosome Start End Strand Distance 0 chr1 4818 4819 + 0 1 chr1 4818 4819 - 0 Actual Chromosome Start End Strand Distance 0 chr1 4818 4819 + 0 1 chr1 4818 4819 - 0 Expected Chromosome Start End Strand Distance 0 chr1 4818 4819 + 0 1 chr1 4818 4819 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp45wjwbre/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp45wjwbre/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphw854rxh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphw854rxh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ulio798/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ulio798/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg3uop8xp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg3uop8xp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxcg4k1yh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxcg4k1yh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvblttyu1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvblttyu1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9q5vvwr6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9q5vvwr6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5kedixoh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5kedixoh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4l_1qugq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4l_1qugq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqfiuym6c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqfiuym6c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuukhi1y9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuukhi1y9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzqq6mbqt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzqq6mbqt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpde4qctra/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpde4qctra/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjks7tjfg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjks7tjfg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd440kobs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd440kobs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_o7i5cpg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_o7i5cpg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0iwj1vjf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0iwj1vjf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp06jmi6kd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp06jmi6kd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwri7j296/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwri7j296/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0z3a3md2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0z3a3md2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsgmm3g12/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsgmm3g12/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi1eekwcg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi1eekwcg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuq46t_n2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuq46t_n2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9a36ac1h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9a36ac1h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz3_q_fm3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz3_q_fm3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc0tu3iz8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc0tu3iz8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpai4sh0lw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpai4sh0lw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqtfirozd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqtfirozd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp_3oj01z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_3oj01z/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp64n_i76w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp64n_i76w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnqxriwak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnqxriwak/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6sazj72a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6sazj72a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqnla6uxu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqnla6uxu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyoww2yvf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyoww2yvf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqdefcuk1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqdefcuk1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwurcc3t0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwurcc3t0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphbolcm6o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphbolcm6o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgyf_568y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgyf_568y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0b4ztlf0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0b4ztlf0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp609d_9le/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp609d_9le/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2p_zie79/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2p_zie79/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdkls9vg1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdkls9vg1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpndn05zlb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpndn05zlb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc99_2j8t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc99_2j8t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzvfybb5g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzvfybb5g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8kpmb6mr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8kpmb6mr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp93ttg16h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp93ttg16h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb66ft48b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb66ft48b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt22nlax2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt22nlax2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn19r370_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn19r370_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpds2l86zh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpds2l86zh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4hmoz0s1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4hmoz0s1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwb5epvn_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwb5epvn_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqloryr95/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqloryr95/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwqu00lqz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwqu00lqz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdf_lmd5h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdf_lmd5h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ya037l2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ya037l2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplwocfoon/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplwocfoon/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj0k_dl7l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj0k_dl7l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl0sdgh8s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0sdgh8s/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmputhng20_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmputhng20_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgmg9ukdv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgmg9ukdv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeh3ukw95/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeh3ukw95/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbeoda5lq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbeoda5lq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdidhjvyn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdidhjvyn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi8ui9cve/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi8ui9cve/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqkky53ne/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqkky53ne/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfugb4l1v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfugb4l1v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprtj4a3_n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprtj4a3_n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzdw22bef/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzdw22bef/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2015x0a2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2015x0a2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0aca2wu2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0aca2wu2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4819 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4819 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4819 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 4819 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 4819 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 4819 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqmxyrjom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqmxyrjom/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphwi82b1q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphwi82b1q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe4783n5e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe4783n5e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4819 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4819 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4819 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 4819 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 4819 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 4819 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa0j7b45l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa0j7b45l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcnwvoeej/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcnwvoeej/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm9mlqp44/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm9mlqp44/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgi2hvdbc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgi2hvdbc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpddgnlo62/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpddgnlo62/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbl7pj44z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbl7pj44z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpme1ocmz1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpme1ocmz1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxw6f7k6d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxw6f7k6d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp98e_udi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp98e_udi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4819 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4819 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4819 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 4819 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 4819 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 4819 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgpenexjo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgpenexjo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl0pzixzq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0pzixzq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8asu504v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8asu504v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvmnzjw4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvmnzjw4v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt3db_gbg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt3db_gbg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcclzi94l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcclzi94l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg7nnezbe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7nnezbe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm_3693n9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm_3693n9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpviy2jeic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpviy2jeic/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnxggcc6f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnxggcc6f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvwvisxuc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvwvisxuc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm6syf813/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm6syf813/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxfya4zat/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxfya4zat/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwuod5spt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwuod5spt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpql4r_yvn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpql4r_yvn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8om71bsx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8om71bsx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa7btxsis/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa7btxsis/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzlc_thd5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzlc_thd5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxlfcj73n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxlfcj73n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz8p92rqo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz8p92rqo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5la379oe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5la379oe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprnanisxx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprnanisxx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvcm9hv0k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvcm9hv0k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfyc97g3k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfyc97g3k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp311eqcov/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp311eqcov/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpinh89ga_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpinh89ga_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6o7hl6y9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6o7hl6y9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3wiyik9c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3wiyik9c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvy5kdoeu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvy5kdoeu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp277bumme/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp277bumme/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_7gl53kh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7gl53kh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp29so595l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp29so595l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx34roy8s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx34roy8s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps25d2vld/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps25d2vld/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk6w0orkg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk6w0orkg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1oafzy77/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1oafzy77/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpianryopf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpianryopf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8okexqk4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8okexqk4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6bahr23z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6bahr23z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2yjjoub1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2yjjoub1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpem9988_3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpem9988_3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6cpmi2kn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6cpmi2kn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7mmk5l__/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7mmk5l__/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz619joh6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz619joh6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp41pl5_nf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp41pl5_nf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoq_taanr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoq_taanr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5e82tz0o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5e82tz0o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz71xumy1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz71xumy1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp51je5oeu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp51je5oeu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8y7kzi2v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8y7kzi2v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm5xgussd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm5xgussd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaz5hpbid/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaz5hpbid/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9b4k77c9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9b4k77c9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzpzil7or/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzpzil7or/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy2h4v1l8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy2h4v1l8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv4ykx_6h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv4ykx_6h/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplf6uyeqi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplf6uyeqi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7c8mzad_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7c8mzad_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuf1fqli0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuf1fqli0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcxn0xabq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcxn0xabq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5hv_o41e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5hv_o41e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpim4go2bt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpim4go2bt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppkvu6vd7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppkvu6vd7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0xw8l_6o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xw8l_6o/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr_r2u21s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr_r2u21s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo5x_193g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo5x_193g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnc4pa99u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnc4pa99u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsrui3lpd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsrui3lpd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_x2z0jyx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_x2z0jyx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwh4eo5by/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwh4eo5by/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx5ab_hp2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx5ab_hp2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpplpabjzi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpplpabjzi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpse9ue4a7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpse9ue4a7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphiq6ubns/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphiq6ubns/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp84sixfrt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp84sixfrt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppb8vhit_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppb8vhit_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpevu2e2b8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpevu2e2b8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp97_rrncd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp97_rrncd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbpz6shom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbpz6shom/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpil93bsy8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpil93bsy8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp322ogaof/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp322ogaof/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu0u7vfpw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu0u7vfpw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpydhhhss5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpydhhhss5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz1hcapx7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz1hcapx7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkzcr0tpc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkzcr0tpc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6yf53a44/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6yf53a44/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzskcs9yd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzskcs9yd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf57hov7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf57hov7q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjoblk1bi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjoblk1bi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmsjr6kqi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmsjr6kqi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwk0ja9rw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwk0ja9rw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_3tram7b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_3tram7b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe8ydbfcn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8ydbfcn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpum3_43so/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpum3_43so/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ze3erj1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ze3erj1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9_xxxhg9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_xxxhg9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpukfueipf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpukfueipf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0wj3ly37/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0wj3ly37/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl58vgffm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl58vgffm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp658u5ziw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp658u5ziw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpibnyzffm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpibnyzffm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ubws44b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ubws44b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1_w9iqkx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1_w9iqkx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpchq_aobf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpchq_aobf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4f_hgnlk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4f_hgnlk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl9cwp412/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl9cwp412/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvtuxacj8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtuxacj8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpatwqmmvm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpatwqmmvm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1vf_3v0j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1vf_3v0j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq9y8483f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9y8483f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp807eecun/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp807eecun/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8zhwufyt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8zhwufyt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv_bo_mvx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv_bo_mvx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfkenh5tx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfkenh5tx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpydmbbt7m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpydmbbt7m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc0exe1sb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc0exe1sb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg6858ty1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg6858ty1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkb_1k3ss/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkb_1k3ss/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxa_2mkgo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxa_2mkgo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe8ofg45g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8ofg45g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe8wd_15n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8wd_15n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5b0l97qh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5b0l97qh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdi_sb2si/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdi_sb2si/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuslstojx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuslstojx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7bovxhj8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7bovxhj8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplunl11ye/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplunl11ye/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3ligy_n3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ligy_n3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdf7s61i3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdf7s61i3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe4oa1ydn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe4oa1ydn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxuu87jaz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxuu87jaz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpilobgwsp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpilobgwsp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu8u57ztb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu8u57ztb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeq9hghsh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeq9hghsh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3u6wyhm7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3u6wyhm7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain24-method_chain24] ___________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGAAYkcmMMnICOYDIYQLQWDIAABPPwPf') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +13 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1327535 | 1332472 | a | 0 | ... | | chr1 | 5022014 | 5023075 | a | 0 | ... | | chr1 | 6583432 | 6592933 | a | 0 | ... | | chr1 | 6432737 | 6442737 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr4 | 1440473 | 1445308 | a | 0 | ... | | chr12 | 421361 | 428229 | a | 0 | ... | | chr13 | 1644236 | 1645944 | a | 0 | ... | | chr19 | 4161340 | 4162579 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 18 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 13 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance, ... (+ 6 more.) ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +13 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 18 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 13 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance, ... (+ 6 more.) ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 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PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') 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PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 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---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _________________________ test_k_nearest_1_vs_nearest __________________________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 @settings( > max_examples=max_examples, deadline=deadline, print_blob=True, suppress_health_check=HealthCheck.all()) tests/test_binary.py:576: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:583: in test_k_nearest_1_vs_nearest result_k = gr.k_nearest(gr2, k=1, strandedness=None, overlap=True, how=None) pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest_1_vs_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:19 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:28 E (and 38 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:24: ValueError ___________ test_three_in_a_row[strandedness_chain41-method_chain41] ___________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkdGQFYgZGR0YGBiCGIgYGACLyAlY=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') _____________________________ test_set_union[same] _____________________________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:134: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:149: in test_set_union result = gr.set_union(gr2, strandedness=strandedness) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_set_union( E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd cat /tmp/tmpfdf12hu8/f1.bed /tmp/tmpfdf12hu8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6990xyi1/f1.bed /tmp/tmp6990xyi1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp10p6535h/f1.bed /tmp/tmp10p6535h/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmp3iamji/f1.bed /tmp/tmpmp3iamji/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxp287q6_/f1.bed /tmp/tmpxp287q6_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2zo85t83/f1.bed /tmp/tmp2zo85t83/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuhri7jn3/f1.bed /tmp/tmpuhri7jn3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplvdmcdyp/f1.bed /tmp/tmplvdmcdyp/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyaf98g9v/f1.bed /tmp/tmpyaf98g9v/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpikt8zkqv/f1.bed /tmp/tmpikt8zkqv/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp86g_ugau/f1.bed /tmp/tmp86g_ugau/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4z067qve/f1.bed /tmp/tmp4z067qve/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxx16kcgj/f1.bed /tmp/tmpxx16kcgj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7oiiu3s3/f1.bed /tmp/tmp7oiiu3s3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfuvo1auo/f1.bed /tmp/tmpfuvo1auo/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7jaozuls/f1.bed /tmp/tmp7jaozuls/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgygou6ib/f1.bed /tmp/tmpgygou6ib/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1nq6qas9/f1.bed /tmp/tmp1nq6qas9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpk_p_0zg9/f1.bed /tmp/tmpk_p_0zg9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu756u4ly/f1.bed /tmp/tmpu756u4ly/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpiquv9zuf/f1.bed /tmp/tmpiquv9zuf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw_grn0br/f1.bed /tmp/tmpw_grn0br/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyo1vnizo/f1.bed /tmp/tmpyo1vnizo/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpy32jj6d2/f1.bed /tmp/tmpy32jj6d2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphld9fws3/f1.bed /tmp/tmphld9fws3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvc_dkm05/f1.bed /tmp/tmpvc_dkm05/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmputx312m7/f1.bed /tmp/tmputx312m7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpk6ilowkx/f1.bed /tmp/tmpk6ilowkx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3tlckcwm/f1.bed /tmp/tmp3tlckcwm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmj21buor/f1.bed /tmp/tmpmj21buor/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnjfzcmkk/f1.bed /tmp/tmpnjfzcmkk/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptf9uucwy/f1.bed /tmp/tmptf9uucwy/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuk8f9knu/f1.bed /tmp/tmpuk8f9knu/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsvil9hrz/f1.bed /tmp/tmpsvil9hrz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw71ndqej/f1.bed /tmp/tmpw71ndqej/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp805u5mfz/f1.bed /tmp/tmp805u5mfz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6600e7tt/f1.bed /tmp/tmp6600e7tt/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_k5kgh1s/f1.bed /tmp/tmp_k5kgh1s/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2_rckbty/f1.bed /tmp/tmp2_rckbty/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnbqi6xca/f1.bed /tmp/tmpnbqi6xca/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuf_eeay0/f1.bed /tmp/tmpuf_eeay0/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfh33cw9x/f1.bed /tmp/tmpfh33cw9x/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpr4nmjihj/f1.bed /tmp/tmpr4nmjihj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0__jbfbl/f1.bed /tmp/tmp0__jbfbl/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpg2p6hovp/f1.bed /tmp/tmpg2p6hovp/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpoc4fi4e3/f1.bed /tmp/tmpoc4fi4e3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfnqzumfn/f1.bed /tmp/tmpfnqzumfn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0rr9nwwr/f1.bed /tmp/tmp0rr9nwwr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcxt63qy7/f1.bed /tmp/tmpcxt63qy7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4hrke7iw/f1.bed /tmp/tmp4hrke7iw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpemd4m6do/f1.bed /tmp/tmpemd4m6do/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_dxriqff/f1.bed /tmp/tmp_dxriqff/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsm673_q6/f1.bed /tmp/tmpsm673_q6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpaxg5fg45/f1.bed /tmp/tmpaxg5fg45/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpztx428rs/f1.bed /tmp/tmpztx428rs/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc9mbhb3o/f1.bed /tmp/tmpc9mbhb3o/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6b_e2b80/f1.bed /tmp/tmp6b_e2b80/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpm32vff6w/f1.bed /tmp/tmpm32vff6w/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwuq58afc/f1.bed /tmp/tmpwuq58afc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkzwhy4v6/f1.bed /tmp/tmpkzwhy4v6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp87zkh2zj/f1.bed /tmp/tmp87zkh2zj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6lru9o2p/f1.bed /tmp/tmp6lru9o2p/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvt7uhm8w/f1.bed /tmp/tmpvt7uhm8w/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8pikphkc/f1.bed /tmp/tmp8pikphkc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptv0pjzim/f1.bed /tmp/tmptv0pjzim/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbevpsl2y/f1.bed /tmp/tmpbevpsl2y/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpby_a30vc/f1.bed /tmp/tmpby_a30vc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjx_58tuj/f1.bed /tmp/tmpjx_58tuj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpelxosu9x/f1.bed /tmp/tmpelxosu9x/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz7md4t1p/f1.bed /tmp/tmpz7md4t1p/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpv_91agma/f1.bed /tmp/tmpv_91agma/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpo2jax25e/f1.bed /tmp/tmpo2jax25e/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkmeypu63/f1.bed /tmp/tmpkmeypu63/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpav56uxl4/f1.bed /tmp/tmpav56uxl4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnnptsrj1/f1.bed /tmp/tmpnnptsrj1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8f445r7k/f1.bed /tmp/tmp8f445r7k/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvhl6xbfx/f1.bed /tmp/tmpvhl6xbfx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2xjnfwo8/f1.bed /tmp/tmp2xjnfwo8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzj9ogxr1/f1.bed /tmp/tmpzj9ogxr1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyz2z9268/f1.bed /tmp/tmpyz2z9268/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplntpfgab/f1.bed /tmp/tmplntpfgab/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpb4uvlkxw/f1.bed /tmp/tmpb4uvlkxw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_affph1m/f1.bed /tmp/tmp_affph1m/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn409kmi4/f1.bed /tmp/tmpn409kmi4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgn3he_24/f1.bed /tmp/tmpgn3he_24/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptyi3qnio/f1.bed /tmp/tmptyi3qnio/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgyaxma8c/f1.bed /tmp/tmpgyaxma8c/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpv_b8ulm2/f1.bed /tmp/tmpv_b8ulm2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjx4jcl9o/f1.bed /tmp/tmpjx4jcl9o/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpb3gsqda4/f1.bed /tmp/tmpb3gsqda4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp67oj5t1f/f1.bed /tmp/tmp67oj5t1f/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp749cwuim/f1.bed /tmp/tmp749cwuim/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn2d9px61/f1.bed /tmp/tmpn2d9px61/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpenfuoac0/f1.bed /tmp/tmpenfuoac0/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpb46u7qhy/f1.bed /tmp/tmpb46u7qhy/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphl0haatp/f1.bed /tmp/tmphl0haatp/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_lnag_j9/f1.bed /tmp/tmp_lnag_j9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzeawsh3f/f1.bed /tmp/tmpzeawsh3f/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqr0b8qrp/f1.bed /tmp/tmpqr0b8qrp/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8vgpcdwh/f1.bed /tmp/tmp8vgpcdwh/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppbe4mlsu/f1.bed /tmp/tmppbe4mlsu/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw7h4jclz/f1.bed /tmp/tmpw7h4jclz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2gn1qm7h/f1.bed /tmp/tmp2gn1qm7h/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7452yhsp/f1.bed /tmp/tmp7452yhsp/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0n_l_g27/f1.bed /tmp/tmp0n_l_g27/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4k9cwx36/f1.bed /tmp/tmp4k9cwx36/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpaqnolmj2/f1.bed /tmp/tmpaqnolmj2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbte3_jqo/f1.bed /tmp/tmpbte3_jqo/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfgtn5c6j/f1.bed /tmp/tmpfgtn5c6j/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4gvcc7tj/f1.bed /tmp/tmp4gvcc7tj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpp848ik9a/f1.bed /tmp/tmpp848ik9a/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps94wri1a/f1.bed /tmp/tmps94wri1a/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqv2jfujz/f1.bed /tmp/tmpqv2jfujz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpg6fcgouw/f1.bed /tmp/tmpg6fcgouw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjtot28sf/f1.bed /tmp/tmpjtot28sf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp66rpn9if/f1.bed /tmp/tmp66rpn9if/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps6wilufy/f1.bed /tmp/tmps6wilufy/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpo6fv4n9h/f1.bed /tmp/tmpo6fv4n9h/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpv093ciu3/f1.bed /tmp/tmpv093ciu3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpogjpypyr/f1.bed /tmp/tmpogjpypyr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3wbnwmwn/f1.bed /tmp/tmp3wbnwmwn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpa4rxyv2f/f1.bed /tmp/tmpa4rxyv2f/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpohho82vo/f1.bed /tmp/tmpohho82vo/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplwus5766/f1.bed /tmp/tmplwus5766/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2b6c7nie/f1.bed /tmp/tmp2b6c7nie/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpluek1qq4/f1.bed /tmp/tmpluek1qq4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpod252iw8/f1.bed /tmp/tmpod252iw8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpk2tg1mbw/f1.bed /tmp/tmpk2tg1mbw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpe84fp52b/f1.bed /tmp/tmpe84fp52b/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl4j1n8be/f1.bed /tmp/tmpl4j1n8be/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0ms2jy44/f1.bed /tmp/tmp0ms2jy44/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwvn14mzs/f1.bed /tmp/tmpwvn14mzs/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpiu9rp_zn/f1.bed /tmp/tmpiu9rp_zn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpalpec5kv/f1.bed /tmp/tmpalpec5kv/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1vizs59d/f1.bed /tmp/tmp1vizs59d/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpahelets8/f1.bed /tmp/tmpahelets8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3t0i_j7y/f1.bed /tmp/tmp3t0i_j7y/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpd07tujnc/f1.bed /tmp/tmpd07tujnc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpg0wunfx3/f1.bed /tmp/tmpg0wunfx3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi1ngwfhv/f1.bed /tmp/tmpi1ngwfhv/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmgoec71o/f1.bed /tmp/tmpmgoec71o/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph8on1r02/f1.bed /tmp/tmph8on1r02/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyt7uv8mv/f1.bed /tmp/tmpyt7uv8mv/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpre8_oa57/f1.bed /tmp/tmpre8_oa57/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0acmob9n/f1.bed /tmp/tmp0acmob9n/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpva9z5so8/f1.bed /tmp/tmpva9z5so8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpunguciau/f1.bed /tmp/tmpunguciau/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmputugvlb2/f1.bed /tmp/tmputugvlb2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcel89fls/f1.bed /tmp/tmpcel89fls/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplrv2yfnd/f1.bed /tmp/tmplrv2yfnd/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjphkh4s_/f1.bed /tmp/tmpjphkh4s_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4umb63r6/f1.bed /tmp/tmp4umb63r6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj8sypm2r/f1.bed /tmp/tmpj8sypm2r/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf97serkl/f1.bed /tmp/tmpf97serkl/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfk426uu0/f1.bed /tmp/tmpfk426uu0/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw41hazxp/f1.bed /tmp/tmpw41hazxp/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6u1ah1mb/f1.bed /tmp/tmp6u1ah1mb/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpeuwy50ll/f1.bed /tmp/tmpeuwy50ll/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9imztbhc/f1.bed /tmp/tmp9imztbhc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpd420v01k/f1.bed /tmp/tmpd420v01k/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpycyb0pqe/f1.bed /tmp/tmpycyb0pqe/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2s030ria/f1.bed /tmp/tmp2s030ria/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1j2sqsv6/f1.bed /tmp/tmp1j2sqsv6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpk_uge7fl/f1.bed /tmp/tmpk_uge7fl/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdayoiqj7/f1.bed /tmp/tmpdayoiqj7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7sdhgpwm/f1.bed /tmp/tmp7sdhgpwm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpiun7cmq3/f1.bed /tmp/tmpiun7cmq3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpy7w1tl0r/f1.bed /tmp/tmpy7w1tl0r/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptd19kimj/f1.bed /tmp/tmptd19kimj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphk6qmp8_/f1.bed /tmp/tmphk6qmp8_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzi5o0i4p/f1.bed /tmp/tmpzi5o0i4p/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbtdcuc5i/f1.bed /tmp/tmpbtdcuc5i/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4_om27l4/f1.bed /tmp/tmp4_om27l4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuzwcojfd/f1.bed /tmp/tmpuzwcojfd/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpv0dn_9pb/f1.bed /tmp/tmpv0dn_9pb/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7hl12rjt/f1.bed /tmp/tmp7hl12rjt/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj793cpl7/f1.bed /tmp/tmpj793cpl7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvvxfj9ko/f1.bed /tmp/tmpvvxfj9ko/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptdu3yhcc/f1.bed /tmp/tmptdu3yhcc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8ta_lt4_/f1.bed /tmp/tmp8ta_lt4_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4zkitjxh/f1.bed /tmp/tmp4zkitjxh/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5dspx_ly/f1.bed /tmp/tmp5dspx_ly/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpb22ew16d/f1.bed /tmp/tmpb22ew16d/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpevnk3wcb/f1.bed /tmp/tmpevnk3wcb/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphp4q7oyl/f1.bed /tmp/tmphp4q7oyl/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_wtyjk5a/f1.bed /tmp/tmp_wtyjk5a/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcz77v86p/f1.bed /tmp/tmpcz77v86p/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3dk3gkt2/f1.bed /tmp/tmp3dk3gkt2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphh3bswcb/f1.bed /tmp/tmphh3bswcb/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2ulizzhe/f1.bed /tmp/tmp2ulizzhe/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpimytkyn0/f1.bed /tmp/tmpimytkyn0/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpf6j3djq3/f1.bed /tmp/tmpf6j3djq3/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3bd1qz5t/f1.bed /tmp/tmp3bd1qz5t/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7x44ghil/f1.bed /tmp/tmp7x44ghil/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpga7cfl1q/f1.bed /tmp/tmpga7cfl1q/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5qdtj6gt/f1.bed /tmp/tmp5qdtj6gt/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpoww9c_31/f1.bed /tmp/tmpoww9c_31/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnu55qixs/f1.bed /tmp/tmpnu55qixs/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt5twh0e9/f1.bed /tmp/tmpt5twh0e9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphn4_srzs/f1.bed /tmp/tmphn4_srzs/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2r4vsh7s/f1.bed /tmp/tmp2r4vsh7s/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi1kd9n3r/f1.bed /tmp/tmpi1kd9n3r/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9zy2cibg/f1.bed /tmp/tmp9zy2cibg/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplzjo1bjj/f1.bed /tmp/tmplzjo1bjj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxv7tz3is/f1.bed /tmp/tmpxv7tz3is/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpa2b2qhsc/f1.bed /tmp/tmpa2b2qhsc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpr2yhdack/f1.bed /tmp/tmpr2yhdack/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi3n816ms/f1.bed /tmp/tmpi3n816ms/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpx5vco3oo/f1.bed /tmp/tmpx5vco3oo/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2dowdy6w/f1.bed /tmp/tmp2dowdy6w/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4hvism96/f1.bed /tmp/tmp4hvism96/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyymz6w91/f1.bed /tmp/tmpyymz6w91/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0k4o85jr/f1.bed /tmp/tmp0k4o85jr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3f8azrsn/f1.bed /tmp/tmp3f8azrsn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpo3pwmlqf/f1.bed /tmp/tmpo3pwmlqf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpg269tzh5/f1.bed /tmp/tmpg269tzh5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgikahul1/f1.bed /tmp/tmpgikahul1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpow3h1e67/f1.bed /tmp/tmpow3h1e67/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmph13lh609/f1.bed /tmp/tmph13lh609/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptw5uyghj/f1.bed /tmp/tmptw5uyghj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpymsx420k/f1.bed /tmp/tmpymsx420k/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpepbvbk4c/f1.bed /tmp/tmpepbvbk4c/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuwrxd167/f1.bed /tmp/tmpuwrxd167/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprgg3fotj/f1.bed /tmp/tmprgg3fotj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9kdi1wb1/f1.bed /tmp/tmp9kdi1wb1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcgn1b3m7/f1.bed /tmp/tmpcgn1b3m7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp13icns_4/f1.bed /tmp/tmp13icns_4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxxv21ueu/f1.bed /tmp/tmpxxv21ueu/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdimpa1d0/f1.bed /tmp/tmpdimpa1d0/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdyj5i1xt/f1.bed /tmp/tmpdyj5i1xt/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9driyaof/f1.bed /tmp/tmp9driyaof/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc7_kw05q/f1.bed /tmp/tmpc7_kw05q/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp44sro2bj/f1.bed /tmp/tmp44sro2bj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3a5pcbqk/f1.bed /tmp/tmp3a5pcbqk/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5hs0sotz/f1.bed /tmp/tmp5hs0sotz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppvwt3e45/f1.bed /tmp/tmppvwt3e45/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwbc3er4k/f1.bed /tmp/tmpwbc3er4k/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxu4lg5wd/f1.bed /tmp/tmpxu4lg5wd/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp334kcpxv/f1.bed /tmp/tmp334kcpxv/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp449k56t4/f1.bed /tmp/tmp449k56t4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzwi6kid6/f1.bed /tmp/tmpzwi6kid6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxgju_cmf/f1.bed /tmp/tmpxgju_cmf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5kjgx05h/f1.bed /tmp/tmp5kjgx05h/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8cu451ux/f1.bed /tmp/tmp8cu451ux/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpicqm63iq/f1.bed /tmp/tmpicqm63iq/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwbxsfhx4/f1.bed /tmp/tmpwbxsfhx4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp80ku6l08/f1.bed /tmp/tmp80ku6l08/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu3kizc7o/f1.bed /tmp/tmpu3kizc7o/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0skydg63/f1.bed /tmp/tmp0skydg63/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfga9weqr/f1.bed /tmp/tmpfga9weqr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7og994dt/f1.bed /tmp/tmp7og994dt/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjjiq6bff/f1.bed /tmp/tmpjjiq6bff/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpk05sv8wv/f1.bed /tmp/tmpk05sv8wv/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwzqcdwlo/f1.bed /tmp/tmpwzqcdwlo/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpergehg__/f1.bed /tmp/tmpergehg__/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp15b9n0s_/f1.bed /tmp/tmp15b9n0s_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprmpok44s/f1.bed /tmp/tmprmpok44s/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5z8zp1bf/f1.bed /tmp/tmp5z8zp1bf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqptkvwrb/f1.bed /tmp/tmpqptkvwrb/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppvd8um1d/f1.bed /tmp/tmppvd8um1d/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc2rmxiao/f1.bed /tmp/tmpc2rmxiao/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7gld84ib/f1.bed /tmp/tmp7gld84ib/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgpun6o2_/f1.bed /tmp/tmpgpun6o2_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5or0_o9b/f1.bed /tmp/tmp5or0_o9b/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp500n7m_7/f1.bed /tmp/tmp500n7m_7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl23xazkj/f1.bed /tmp/tmpl23xazkj/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_uownq0n/f1.bed /tmp/tmp_uownq0n/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphl5foqvm/f1.bed /tmp/tmphl5foqvm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi6a1lfep/f1.bed /tmp/tmpi6a1lfep/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpag45xd0y/f1.bed /tmp/tmpag45xd0y/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjirgc_hm/f1.bed /tmp/tmpjirgc_hm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpooo3xv_7/f1.bed /tmp/tmpooo3xv_7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprhmvbk_q/f1.bed /tmp/tmprhmvbk_q/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphi9km7is/f1.bed /tmp/tmphi9km7is/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw1kh2kda/f1.bed /tmp/tmpw1kh2kda/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpe2xmron7/f1.bed /tmp/tmpe2xmron7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp08molukk/f1.bed /tmp/tmp08molukk/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqwgnv6gu/f1.bed /tmp/tmpqwgnv6gu/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpimaj_l36/f1.bed /tmp/tmpimaj_l36/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi3e2bzkr/f1.bed /tmp/tmpi3e2bzkr/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkkth4t19/f1.bed /tmp/tmpkkth4t19/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplotci2lt/f1.bed /tmp/tmplotci2lt/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn36hz7w7/f1.bed /tmp/tmpn36hz7w7/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyrhopi0t/f1.bed /tmp/tmpyrhopi0t/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpvklbkxqd/f1.bed /tmp/tmpvklbkxqd/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4wvsnb9g/f1.bed /tmp/tmp4wvsnb9g/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpznqesun2/f1.bed /tmp/tmpznqesun2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpo7yrjs8m/f1.bed /tmp/tmpo7yrjs8m/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0azh8wjc/f1.bed /tmp/tmp0azh8wjc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjackncsc/f1.bed /tmp/tmpjackncsc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpse5b7k7f/f1.bed /tmp/tmpse5b7k7f/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpoj94215u/f1.bed /tmp/tmpoj94215u/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpupseq66p/f1.bed /tmp/tmpupseq66p/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpr9ei29p2/f1.bed /tmp/tmpr9ei29p2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzgrd4_re/f1.bed /tmp/tmpzgrd4_re/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphr7vofha/f1.bed /tmp/tmphr7vofha/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpcikg8l0u/f1.bed /tmp/tmpcikg8l0u/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpskznzwos/f1.bed /tmp/tmpskznzwos/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmperjdvj4c/f1.bed /tmp/tmperjdvj4c/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwj_kziyw/f1.bed /tmp/tmpwj_kziyw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplsm6v7f9/f1.bed /tmp/tmplsm6v7f9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkxwywl33/f1.bed /tmp/tmpkxwywl33/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpm1_h8ylc/f1.bed /tmp/tmpm1_h8ylc/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpi6hoqca4/f1.bed /tmp/tmpi6hoqca4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpff0yh_gw/f1.bed /tmp/tmpff0yh_gw/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp0irxtek5/f1.bed /tmp/tmp0irxtek5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp501_8h66/f1.bed /tmp/tmp501_8h66/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4slrfnym/f1.bed /tmp/tmp4slrfnym/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmperembxl6/f1.bed /tmp/tmperembxl6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpbh6p8q1l/f1.bed /tmp/tmpbh6p8q1l/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt5v_q7vm/f1.bed /tmp/tmpt5v_q7vm/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptr_hwc_6/f1.bed /tmp/tmptr_hwc_6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfsxqd6xo/f1.bed /tmp/tmpfsxqd6xo/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4b44y1x6/f1.bed /tmp/tmp4b44y1x6/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpof2w618t/f1.bed /tmp/tmpof2w618t/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwh01ycay/f1.bed /tmp/tmpwh01ycay/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc8jrmo_d/f1.bed /tmp/tmpc8jrmo_d/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5h5tzpd9/f1.bed /tmp/tmp5h5tzpd9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp83xue90q/f1.bed /tmp/tmp83xue90q/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw600jni5/f1.bed /tmp/tmpw600jni5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppb0jji4j/f1.bed /tmp/tmppb0jji4j/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn0euhdl1/f1.bed /tmp/tmpn0euhdl1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj70ljo66/f1.bed /tmp/tmpj70ljo66/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpywavpfu_/f1.bed /tmp/tmpywavpfu_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpe8lillpb/f1.bed /tmp/tmpe8lillpb/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpc9jvz9ek/f1.bed /tmp/tmpc9jvz9ek/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpgofcrz90/f1.bed /tmp/tmpgofcrz90/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzcikem_e/f1.bed /tmp/tmpzcikem_e/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpef3dv9el/f1.bed /tmp/tmpef3dv9el/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnmk4lq79/f1.bed /tmp/tmpnmk4lq79/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6oh7mj40/f1.bed /tmp/tmp6oh7mj40/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpuf9l3kw9/f1.bed /tmp/tmpuf9l3kw9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpy5r4b7qk/f1.bed /tmp/tmpy5r4b7qk/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyh3pci_8/f1.bed /tmp/tmpyh3pci_8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt2bx6uud/f1.bed /tmp/tmpt2bx6uud/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp75y6wo34/f1.bed /tmp/tmp75y6wo34/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6rg7734j/f1.bed /tmp/tmp6rg7734j/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwkeor0ip/f1.bed /tmp/tmpwkeor0ip/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzlsmu249/f1.bed /tmp/tmpzlsmu249/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw5gi20hn/f1.bed /tmp/tmpw5gi20hn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdmi880ws/f1.bed /tmp/tmpdmi880ws/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj2y1aqpg/f1.bed /tmp/tmpj2y1aqpg/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmcq7e4nh/f1.bed /tmp/tmpmcq7e4nh/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptxb86t35/f1.bed /tmp/tmptxb86t35/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpat2um16x/f1.bed /tmp/tmpat2um16x/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpn1l52hot/f1.bed /tmp/tmpn1l52hot/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp126d71ws/f1.bed /tmp/tmp126d71ws/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpy171cwf5/f1.bed /tmp/tmpy171cwf5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp241h57wv/f1.bed /tmp/tmp241h57wv/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpxt31_2ic/f1.bed /tmp/tmpxt31_2ic/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmplqn_2b02/f1.bed /tmp/tmplqn_2b02/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpjy6krbd_/f1.bed /tmp/tmpjy6krbd_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp4b_wjq1c/f1.bed /tmp/tmp4b_wjq1c/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpinfir899/f1.bed /tmp/tmpinfir899/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpln1tdvnf/f1.bed /tmp/tmpln1tdvnf/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprbkh1o73/f1.bed /tmp/tmprbkh1o73/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpw68aorbg/f1.bed /tmp/tmpw68aorbg/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpr4aojgah/f1.bed /tmp/tmpr4aojgah/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpzp9ksurn/f1.bed /tmp/tmpzp9ksurn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwoza0_p4/f1.bed /tmp/tmpwoza0_p4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6fdwupj2/f1.bed /tmp/tmp6fdwupj2/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8guurg70/f1.bed /tmp/tmp8guurg70/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps_atl3x9/f1.bed /tmp/tmps_atl3x9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp82cbzo3x/f1.bed /tmp/tmp82cbzo3x/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmppcv0v1mq/f1.bed /tmp/tmppcv0v1mq/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmptia8ccvl/f1.bed /tmp/tmptia8ccvl/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmprziicd6s/f1.bed /tmp/tmprziicd6s/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkw83ecr8/f1.bed /tmp/tmpkw83ecr8/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpq4jan811/f1.bed /tmp/tmpq4jan811/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________________________ test_subtraction[opposite] __________________________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness = 'opposite' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", ["same", "opposite", False]) # tests/test_binary.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:308: in test_subtraction result = gr.subtract(gr2, strandedness=strandedness) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_subtraction( E strandedness='opposite', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9zlvloup/f1.bed -b /tmp/tmp9zlvloup/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbmgbjj25/f1.bed -b /tmp/tmpbmgbjj25/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4ysnvkz4/f1.bed -b /tmp/tmp4ysnvkz4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfyo40u4g/f1.bed -b /tmp/tmpfyo40u4g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpi3ilnx89/f1.bed -b /tmp/tmpi3ilnx89/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkf87lehk/f1.bed -b /tmp/tmpkf87lehk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4lte28st/f1.bed -b /tmp/tmp4lte28st/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplv2zjw7q/f1.bed -b /tmp/tmplv2zjw7q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmc4cw7cb/f1.bed -b /tmp/tmpmc4cw7cb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpp28qfks_/f1.bed -b /tmp/tmpp28qfks_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8obnysmp/f1.bed -b /tmp/tmp8obnysmp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4wi7u4uo/f1.bed -b /tmp/tmp4wi7u4uo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqs1lnb_f/f1.bed -b /tmp/tmpqs1lnb_f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpivu28xdv/f1.bed -b /tmp/tmpivu28xdv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp10wzys89/f1.bed -b /tmp/tmp10wzys89/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppk9sufub/f1.bed -b /tmp/tmppk9sufub/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4eohd79d/f1.bed -b /tmp/tmp4eohd79d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmprvhq95zi/f1.bed -b /tmp/tmprvhq95zi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpd6gpbqvx/f1.bed -b /tmp/tmpd6gpbqvx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpph1ywh4j/f1.bed -b /tmp/tmpph1ywh4j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpehfql3pu/f1.bed -b /tmp/tmpehfql3pu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpcak7djth/f1.bed -b /tmp/tmpcak7djth/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpat40iioj/f1.bed -b /tmp/tmpat40iioj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpchgac80_/f1.bed -b /tmp/tmpchgac80_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0j8cec0q/f1.bed -b /tmp/tmp0j8cec0q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmptvr60zqz/f1.bed -b /tmp/tmptvr60zqz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2xccfgje/f1.bed -b /tmp/tmp2xccfgje/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1fy_v7aa/f1.bed -b /tmp/tmp1fy_v7aa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpc_gpsu_q/f1.bed -b /tmp/tmpc_gpsu_q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzk129v_x/f1.bed -b /tmp/tmpzk129v_x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0xt5uadj/f1.bed -b /tmp/tmp0xt5uadj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_ux_7lgd/f1.bed -b /tmp/tmp_ux_7lgd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpcwy8yial/f1.bed -b /tmp/tmpcwy8yial/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0hpbyw2i/f1.bed -b /tmp/tmp0hpbyw2i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfi855fny/f1.bed -b /tmp/tmpfi855fny/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdeaqvikv/f1.bed -b /tmp/tmpdeaqvikv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8oqxp78a/f1.bed -b /tmp/tmp8oqxp78a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmph7qhgutq/f1.bed -b /tmp/tmph7qhgutq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjpd5c4gy/f1.bed -b /tmp/tmpjpd5c4gy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpw3f3j2o9/f1.bed -b /tmp/tmpw3f3j2o9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp03pizc6h/f1.bed -b /tmp/tmp03pizc6h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmprfp20fkz/f1.bed -b /tmp/tmprfp20fkz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp564tx86t/f1.bed -b /tmp/tmp564tx86t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpcmwsqbnd/f1.bed -b /tmp/tmpcmwsqbnd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpezf9gsy0/f1.bed -b /tmp/tmpezf9gsy0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4kh1wmdi/f1.bed -b /tmp/tmp4kh1wmdi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpt6uxi38n/f1.bed -b /tmp/tmpt6uxi38n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7v99p320/f1.bed -b /tmp/tmp7v99p320/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkkvygco5/f1.bed -b /tmp/tmpkkvygco5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpuezrm6zw/f1.bed -b /tmp/tmpuezrm6zw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpure1oeof/f1.bed -b /tmp/tmpure1oeof/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpa101crxk/f1.bed -b /tmp/tmpa101crxk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmegjw62l/f1.bed -b /tmp/tmpmegjw62l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4o89zl4j/f1.bed -b /tmp/tmp4o89zl4j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_pusfuzw/f1.bed -b /tmp/tmp_pusfuzw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1q7dcyxo/f1.bed -b /tmp/tmp1q7dcyxo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpyw7l8u_o/f1.bed -b /tmp/tmpyw7l8u_o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppcmaa4mv/f1.bed -b /tmp/tmppcmaa4mv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpnjmu6lgg/f1.bed -b /tmp/tmpnjmu6lgg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp603joimt/f1.bed -b /tmp/tmp603joimt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1of4mgo3/f1.bed -b /tmp/tmp1of4mgo3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpyia5mbgj/f1.bed -b /tmp/tmpyia5mbgj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp149ddmmt/f1.bed -b /tmp/tmp149ddmmt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpznjp_jkj/f1.bed -b /tmp/tmpznjp_jkj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7888gdzd/f1.bed -b /tmp/tmp7888gdzd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgoaqe8b6/f1.bed -b /tmp/tmpgoaqe8b6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwt74aqyv/f1.bed -b /tmp/tmpwt74aqyv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0z1r7do7/f1.bed -b /tmp/tmp0z1r7do7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwcimvdad/f1.bed -b /tmp/tmpwcimvdad/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6hk_dxv2/f1.bed -b /tmp/tmp6hk_dxv2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbqb1fov0/f1.bed -b /tmp/tmpbqb1fov0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbckek6_v/f1.bed -b /tmp/tmpbckek6_v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpe045bilq/f1.bed -b /tmp/tmpe045bilq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdm6yh_0j/f1.bed -b /tmp/tmpdm6yh_0j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpw0nrp01h/f1.bed -b /tmp/tmpw0nrp01h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp84zescbu/f1.bed -b /tmp/tmp84zescbu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvqjhk3pf/f1.bed -b /tmp/tmpvqjhk3pf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5srse0rq/f1.bed -b /tmp/tmp5srse0rq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmprvc7hebl/f1.bed -b /tmp/tmprvc7hebl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp57i937wa/f1.bed -b /tmp/tmp57i937wa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpo6e29_rg/f1.bed -b /tmp/tmpo6e29_rg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjbrvya_2/f1.bed -b /tmp/tmpjbrvya_2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2ywnlqdi/f1.bed -b /tmp/tmp2ywnlqdi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkrziv3ww/f1.bed -b /tmp/tmpkrziv3ww/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpf9w2gjxz/f1.bed -b /tmp/tmpf9w2gjxz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbp7cb5qt/f1.bed -b /tmp/tmpbp7cb5qt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpi69t_tf9/f1.bed -b /tmp/tmpi69t_tf9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpr265u1su/f1.bed -b /tmp/tmpr265u1su/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdfq12lg0/f1.bed -b /tmp/tmpdfq12lg0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_9hfcbfw/f1.bed -b /tmp/tmp_9hfcbfw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp07kr6582/f1.bed -b /tmp/tmp07kr6582/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpu4_33ja3/f1.bed -b /tmp/tmpu4_33ja3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpxgxs6w16/f1.bed -b /tmp/tmpxgxs6w16/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpl1bamas0/f1.bed -b /tmp/tmpl1bamas0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7egawrtl/f1.bed -b /tmp/tmp7egawrtl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpclxw9yg_/f1.bed -b /tmp/tmpclxw9yg_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqrz8rxz0/f1.bed -b /tmp/tmpqrz8rxz0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpiakjl3h8/f1.bed -b /tmp/tmpiakjl3h8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmn7v04ug/f1.bed -b /tmp/tmpmn7v04ug/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpj5ihed_c/f1.bed -b /tmp/tmpj5ihed_c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpje2jptkm/f1.bed -b /tmp/tmpje2jptkm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpj44ggfjy/f1.bed -b /tmp/tmpj44ggfjy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpaz6rwn9i/f1.bed -b /tmp/tmpaz6rwn9i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpntik0b0q/f1.bed -b /tmp/tmpntik0b0q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppqqrxl45/f1.bed -b /tmp/tmppqqrxl45/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6vq2pkjg/f1.bed -b /tmp/tmp6vq2pkjg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0k9y1koz/f1.bed -b /tmp/tmp0k9y1koz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpucwnle18/f1.bed -b /tmp/tmpucwnle18/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpyqq5a4pd/f1.bed -b /tmp/tmpyqq5a4pd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9z7bcl7m/f1.bed -b /tmp/tmp9z7bcl7m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6f33hwwa/f1.bed -b /tmp/tmp6f33hwwa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp54fdilj8/f1.bed -b /tmp/tmp54fdilj8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpagiveb4n/f1.bed -b /tmp/tmpagiveb4n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpeaw3ky5q/f1.bed -b /tmp/tmpeaw3ky5q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp86nk0e1w/f1.bed -b /tmp/tmp86nk0e1w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5409x7gk/f1.bed -b /tmp/tmp5409x7gk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp52sxtz1a/f1.bed -b /tmp/tmp52sxtz1a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmposi49hjv/f1.bed -b /tmp/tmposi49hjv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppby49v69/f1.bed -b /tmp/tmppby49v69/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8l8ch967/f1.bed -b /tmp/tmp8l8ch967/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplkxyi7bq/f1.bed -b /tmp/tmplkxyi7bq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpt96sc5va/f1.bed -b /tmp/tmpt96sc5va/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5hrn1v24/f1.bed -b /tmp/tmp5hrn1v24/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_ap935xq/f1.bed -b /tmp/tmp_ap935xq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp207n3ixf/f1.bed -b /tmp/tmp207n3ixf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0rv6yz4a/f1.bed -b /tmp/tmp0rv6yz4a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp59ej4d_o/f1.bed -b /tmp/tmp59ej4d_o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp22kb6an7/f1.bed -b /tmp/tmp22kb6an7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphnaoj7xo/f1.bed -b /tmp/tmphnaoj7xo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmprxmstwkp/f1.bed -b /tmp/tmprxmstwkp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpthuepn0k/f1.bed -b /tmp/tmpthuepn0k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp620s12o0/f1.bed -b /tmp/tmp620s12o0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp67929oi0/f1.bed -b /tmp/tmp67929oi0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7xk9rbn4/f1.bed -b /tmp/tmp7xk9rbn4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8msw37o6/f1.bed -b /tmp/tmp8msw37o6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2_mebje_/f1.bed -b /tmp/tmp2_mebje_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1n_o1riv/f1.bed -b /tmp/tmp1n_o1riv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplm4cp_q7/f1.bed -b /tmp/tmplm4cp_q7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2lee_e9r/f1.bed -b /tmp/tmp2lee_e9r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpsabrozqa/f1.bed -b /tmp/tmpsabrozqa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjql8pvd7/f1.bed -b /tmp/tmpjql8pvd7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpj3jizmh2/f1.bed -b /tmp/tmpj3jizmh2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7lk1pb9o/f1.bed -b /tmp/tmp7lk1pb9o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpb1arrzoq/f1.bed -b /tmp/tmpb1arrzoq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpap_1ff4u/f1.bed -b /tmp/tmpap_1ff4u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpcgvy041e/f1.bed -b /tmp/tmpcgvy041e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpz77s79zx/f1.bed -b /tmp/tmpz77s79zx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwjjjefbr/f1.bed -b /tmp/tmpwjjjefbr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpl4ha4ejf/f1.bed -b /tmp/tmpl4ha4ejf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpufnbwaar/f1.bed -b /tmp/tmpufnbwaar/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmprqn0du76/f1.bed -b /tmp/tmprqn0du76/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_6160s1y/f1.bed -b /tmp/tmp_6160s1y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppoc1am1r/f1.bed -b /tmp/tmppoc1am1r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdrkfrpqt/f1.bed -b /tmp/tmpdrkfrpqt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpysht0urf/f1.bed -b /tmp/tmpysht0urf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpoxqyhttg/f1.bed -b /tmp/tmpoxqyhttg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6gm80o0n/f1.bed -b /tmp/tmp6gm80o0n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8jzdw31l/f1.bed -b /tmp/tmp8jzdw31l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpyfaackm1/f1.bed -b /tmp/tmpyfaackm1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpj81udi5q/f1.bed -b /tmp/tmpj81udi5q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpz6ljtjwn/f1.bed -b /tmp/tmpz6ljtjwn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpf627ifh9/f1.bed -b /tmp/tmpf627ifh9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbb3v7y3m/f1.bed -b /tmp/tmpbb3v7y3m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvi0e6fci/f1.bed -b /tmp/tmpvi0e6fci/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpcyi8j7qj/f1.bed -b /tmp/tmpcyi8j7qj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0395ccbz/f1.bed -b /tmp/tmp0395ccbz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpe4genw3d/f1.bed -b /tmp/tmpe4genw3d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzsakn2gk/f1.bed -b /tmp/tmpzsakn2gk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphdarypp0/f1.bed -b /tmp/tmphdarypp0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4aorfmo3/f1.bed -b /tmp/tmp4aorfmo3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfs3jogwv/f1.bed -b /tmp/tmpfs3jogwv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpunqbp7er/f1.bed -b /tmp/tmpunqbp7er/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmps9_ld1tn/f1.bed -b /tmp/tmps9_ld1tn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjlnlprf3/f1.bed -b /tmp/tmpjlnlprf3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpljt9zyzf/f1.bed -b /tmp/tmpljt9zyzf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp53b2cv1n/f1.bed -b /tmp/tmp53b2cv1n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5a2plyah/f1.bed -b /tmp/tmp5a2plyah/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpq6cthxay/f1.bed -b /tmp/tmpq6cthxay/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpb1rfzuwp/f1.bed -b /tmp/tmpb1rfzuwp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpw60roke4/f1.bed -b /tmp/tmpw60roke4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0rtpx40m/f1.bed -b /tmp/tmp0rtpx40m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfo1q_ihh/f1.bed -b /tmp/tmpfo1q_ihh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpxgseesle/f1.bed -b /tmp/tmpxgseesle/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpou44dg_3/f1.bed -b /tmp/tmpou44dg_3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpko6p2y__/f1.bed -b /tmp/tmpko6p2y__/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpud7pki53/f1.bed -b /tmp/tmpud7pki53/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplcf2emq9/f1.bed -b /tmp/tmplcf2emq9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbk5erjyy/f1.bed -b /tmp/tmpbk5erjyy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3od1m8b_/f1.bed -b /tmp/tmp3od1m8b_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpsvaq3fd7/f1.bed -b /tmp/tmpsvaq3fd7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpre9yod5l/f1.bed -b /tmp/tmpre9yod5l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplwq_jcq6/f1.bed -b /tmp/tmplwq_jcq6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpc4j06xa3/f1.bed -b /tmp/tmpc4j06xa3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpub9941wg/f1.bed -b /tmp/tmpub9941wg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvt4rhxia/f1.bed -b /tmp/tmpvt4rhxia/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3jflapvw/f1.bed -b /tmp/tmp3jflapvw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpiv1lf75d/f1.bed -b /tmp/tmpiv1lf75d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpr3y7rhqt/f1.bed -b /tmp/tmpr3y7rhqt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp73j8u6dp/f1.bed -b /tmp/tmp73j8u6dp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpreuzd9gn/f1.bed -b /tmp/tmpreuzd9gn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7a753cn_/f1.bed -b /tmp/tmp7a753cn_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpezohp9r0/f1.bed -b /tmp/tmpezohp9r0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpi_cld34r/f1.bed -b /tmp/tmpi_cld34r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6nmi66vp/f1.bed -b /tmp/tmp6nmi66vp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpknf7yw27/f1.bed -b /tmp/tmpknf7yw27/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpoiefhd9k/f1.bed -b /tmp/tmpoiefhd9k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphxux04dp/f1.bed -b /tmp/tmphxux04dp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6r695avi/f1.bed -b /tmp/tmp6r695avi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2qj8rxuu/f1.bed -b /tmp/tmp2qj8rxuu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdr56a04d/f1.bed -b /tmp/tmpdr56a04d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2lkogw2o/f1.bed -b /tmp/tmp2lkogw2o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwn8rllea/f1.bed -b /tmp/tmpwn8rllea/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9dk9q3ce/f1.bed -b /tmp/tmp9dk9q3ce/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkzoieedp/f1.bed -b /tmp/tmpkzoieedp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9tgngixk/f1.bed -b /tmp/tmp9tgngixk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmz99i90v/f1.bed -b /tmp/tmpmz99i90v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplr6pqbvw/f1.bed -b /tmp/tmplr6pqbvw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8657nlve/f1.bed -b /tmp/tmp8657nlve/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8ximsefh/f1.bed -b /tmp/tmp8ximsefh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpk0c7ygs3/f1.bed -b /tmp/tmpk0c7ygs3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzgc_fzb3/f1.bed -b /tmp/tmpzgc_fzb3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqovu3q7i/f1.bed -b /tmp/tmpqovu3q7i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppmp96eiw/f1.bed -b /tmp/tmppmp96eiw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkywk_rj8/f1.bed -b /tmp/tmpkywk_rj8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2cncrwp2/f1.bed -b /tmp/tmp2cncrwp2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_hub3z_d/f1.bed -b /tmp/tmp_hub3z_d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpeufz7c5e/f1.bed -b /tmp/tmpeufz7c5e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpa8lhaoc6/f1.bed -b /tmp/tmpa8lhaoc6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9rovbi4s/f1.bed -b /tmp/tmp9rovbi4s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpg053cijd/f1.bed -b /tmp/tmpg053cijd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp6mgdgv8q/f1.bed -b /tmp/tmp6mgdgv8q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpyrjd3u5q/f1.bed -b /tmp/tmpyrjd3u5q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbj1rb_xz/f1.bed -b /tmp/tmpbj1rb_xz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzj8ronsh/f1.bed -b /tmp/tmpzj8ronsh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplm_flx18/f1.bed -b /tmp/tmplm_flx18/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpuopcki9h/f1.bed -b /tmp/tmpuopcki9h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfj165y1r/f1.bed -b /tmp/tmpfj165y1r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpsu_sogob/f1.bed -b /tmp/tmpsu_sogob/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0rjnj8gb/f1.bed -b /tmp/tmp0rjnj8gb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqxr2m2s3/f1.bed -b /tmp/tmpqxr2m2s3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpmr5hbop3/f1.bed -b /tmp/tmpmr5hbop3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9uf1eo3e/f1.bed -b /tmp/tmp9uf1eo3e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpp7x_t1tl/f1.bed -b /tmp/tmpp7x_t1tl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpc2yrwdsu/f1.bed -b /tmp/tmpc2yrwdsu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp960vhflu/f1.bed -b /tmp/tmp960vhflu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpyv5wcpbj/f1.bed -b /tmp/tmpyv5wcpbj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1er3ty3t/f1.bed -b /tmp/tmp1er3ty3t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphamesdqk/f1.bed -b /tmp/tmphamesdqk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpunixn61u/f1.bed -b /tmp/tmpunixn61u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpcuz2dy12/f1.bed -b /tmp/tmpcuz2dy12/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpao0pf1ow/f1.bed -b /tmp/tmpao0pf1ow/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_kf6orfu/f1.bed -b /tmp/tmp_kf6orfu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpahrdgspb/f1.bed -b /tmp/tmpahrdgspb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphhdbfo7a/f1.bed -b /tmp/tmphhdbfo7a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfh3s8d3k/f1.bed -b /tmp/tmpfh3s8d3k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7ss7mkio/f1.bed -b /tmp/tmp7ss7mkio/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpa2bwrdz_/f1.bed -b /tmp/tmpa2bwrdz_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpe6kn2nfc/f1.bed -b /tmp/tmpe6kn2nfc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7cuohqgs/f1.bed -b /tmp/tmp7cuohqgs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpb91ruu20/f1.bed -b /tmp/tmpb91ruu20/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpktxa7pm9/f1.bed -b /tmp/tmpktxa7pm9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpupkwjots/f1.bed -b /tmp/tmpupkwjots/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjy6wmhyk/f1.bed -b /tmp/tmpjy6wmhyk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbqt3hpp9/f1.bed -b /tmp/tmpbqt3hpp9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzh3e_2ns/f1.bed -b /tmp/tmpzh3e_2ns/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwkmgzvih/f1.bed -b /tmp/tmpwkmgzvih/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkpa7s4ku/f1.bed -b /tmp/tmpkpa7s4ku/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphxv_uvu9/f1.bed -b /tmp/tmphxv_uvu9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplb55biet/f1.bed -b /tmp/tmplb55biet/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpti2n83e2/f1.bed -b /tmp/tmpti2n83e2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7kbsd3q9/f1.bed -b /tmp/tmp7kbsd3q9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpr1wfcxhm/f1.bed -b /tmp/tmpr1wfcxhm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpiwgd44ke/f1.bed -b /tmp/tmpiwgd44ke/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdp90twh6/f1.bed -b /tmp/tmpdp90twh6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpthse0jb3/f1.bed -b /tmp/tmpthse0jb3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmptmbtaksy/f1.bed -b /tmp/tmptmbtaksy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpebwnrm4z/f1.bed -b /tmp/tmpebwnrm4z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpi1uqn4t9/f1.bed -b /tmp/tmpi1uqn4t9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpti1q2vp5/f1.bed -b /tmp/tmpti1q2vp5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpa00cdha1/f1.bed -b /tmp/tmpa00cdha1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqcpvbrp7/f1.bed -b /tmp/tmpqcpvbrp7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpeyqoe8jb/f1.bed -b /tmp/tmpeyqoe8jb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpa37c5wyk/f1.bed -b /tmp/tmpa37c5wyk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpxa3zbgcp/f1.bed -b /tmp/tmpxa3zbgcp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpiw94wb5j/f1.bed -b /tmp/tmpiw94wb5j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpctm434zw/f1.bed -b /tmp/tmpctm434zw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2t551i1o/f1.bed -b /tmp/tmp2t551i1o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpuqobm8bi/f1.bed -b /tmp/tmpuqobm8bi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3oeduztz/f1.bed -b /tmp/tmp3oeduztz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvaqzbjmk/f1.bed -b /tmp/tmpvaqzbjmk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2xremgk0/f1.bed -b /tmp/tmp2xremgk0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzhex1bh6/f1.bed -b /tmp/tmpzhex1bh6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp220xnybd/f1.bed -b /tmp/tmp220xnybd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpayyf9mn7/f1.bed -b /tmp/tmpayyf9mn7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpli2zsf93/f1.bed -b /tmp/tmpli2zsf93/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp73qbuehg/f1.bed -b /tmp/tmp73qbuehg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdlelxv95/f1.bed -b /tmp/tmpdlelxv95/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqac19bm1/f1.bed -b /tmp/tmpqac19bm1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvtqt0enm/f1.bed -b /tmp/tmpvtqt0enm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4dq6ovy_/f1.bed -b /tmp/tmp4dq6ovy_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphak1sqdb/f1.bed -b /tmp/tmphak1sqdb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjlkzxroq/f1.bed -b /tmp/tmpjlkzxroq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpp52_7crb/f1.bed -b /tmp/tmpp52_7crb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpu14qbecf/f1.bed -b /tmp/tmpu14qbecf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppe1m7v3n/f1.bed -b /tmp/tmppe1m7v3n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpblk_rxub/f1.bed -b /tmp/tmpblk_rxub/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjfh7id56/f1.bed -b /tmp/tmpjfh7id56/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpidoyln5q/f1.bed -b /tmp/tmpidoyln5q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmptfm82wb1/f1.bed -b /tmp/tmptfm82wb1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpe2sqteti/f1.bed -b /tmp/tmpe2sqteti/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphfj089pu/f1.bed -b /tmp/tmphfj089pu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpx3dwh1w4/f1.bed -b /tmp/tmpx3dwh1w4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgh2488o5/f1.bed -b /tmp/tmpgh2488o5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpeuch0ayl/f1.bed -b /tmp/tmpeuch0ayl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplavg2yjp/f1.bed -b /tmp/tmplavg2yjp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdvk6ewmd/f1.bed -b /tmp/tmpdvk6ewmd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpq6epa1qg/f1.bed -b /tmp/tmpq6epa1qg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpz4id8t96/f1.bed -b /tmp/tmpz4id8t96/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5vzvrqav/f1.bed -b /tmp/tmp5vzvrqav/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdlh1grot/f1.bed -b /tmp/tmpdlh1grot/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9jze4ljl/f1.bed -b /tmp/tmp9jze4ljl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdw1_l2c6/f1.bed -b /tmp/tmpdw1_l2c6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwuj1jmfv/f1.bed -b /tmp/tmpwuj1jmfv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1nr59f8t/f1.bed -b /tmp/tmp1nr59f8t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpu7vrut0o/f1.bed -b /tmp/tmpu7vrut0o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3hnatmog/f1.bed -b /tmp/tmp3hnatmog/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp80370y1x/f1.bed -b /tmp/tmp80370y1x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp5jp924un/f1.bed -b /tmp/tmp5jp924un/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqb_2hfbd/f1.bed -b /tmp/tmpqb_2hfbd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp94afr4gl/f1.bed -b /tmp/tmp94afr4gl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpx6gnw7yh/f1.bed -b /tmp/tmpx6gnw7yh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp2p1xj9n4/f1.bed -b /tmp/tmp2p1xj9n4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpjfmgis7x/f1.bed -b /tmp/tmpjfmgis7x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpeg2v7o5h/f1.bed -b /tmp/tmpeg2v7o5h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmps4t5r9v7/f1.bed -b /tmp/tmps4t5r9v7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgsjt98ih/f1.bed -b /tmp/tmpgsjt98ih/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpihtvk73a/f1.bed -b /tmp/tmpihtvk73a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqtnvufhe/f1.bed -b /tmp/tmpqtnvufhe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzjzclzxn/f1.bed -b /tmp/tmpzjzclzxn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpv3ja8ea1/f1.bed -b /tmp/tmpv3ja8ea1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4qlta0d6/f1.bed -b /tmp/tmp4qlta0d6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpv86uqb_5/f1.bed -b /tmp/tmpv86uqb_5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpth5_vc_e/f1.bed -b /tmp/tmpth5_vc_e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp4m957w06/f1.bed -b /tmp/tmp4m957w06/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpatswl9o_/f1.bed -b /tmp/tmpatswl9o_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0jt0wxbp/f1.bed -b /tmp/tmp0jt0wxbp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9x5o6yxt/f1.bed -b /tmp/tmp9x5o6yxt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpj8e5f31s/f1.bed -b /tmp/tmpj8e5f31s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmprjs25z67/f1.bed -b /tmp/tmprjs25z67/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpy_gs9ik4/f1.bed -b /tmp/tmpy_gs9ik4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkjvadfoj/f1.bed -b /tmp/tmpkjvadfoj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpsm_kr4tu/f1.bed -b /tmp/tmpsm_kr4tu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpdrgxg8ui/f1.bed -b /tmp/tmpdrgxg8ui/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpw4kv6sbn/f1.bed -b /tmp/tmpw4kv6sbn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpavc8ujgf/f1.bed -b /tmp/tmpavc8ujgf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqytq6bx7/f1.bed -b /tmp/tmpqytq6bx7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmps0ftsqzs/f1.bed -b /tmp/tmps0ftsqzs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpr_lefoqo/f1.bed -b /tmp/tmpr_lefoqo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpv_i1dfyy/f1.bed -b /tmp/tmpv_i1dfyy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbha_tjxw/f1.bed -b /tmp/tmpbha_tjxw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvxgrjtbo/f1.bed -b /tmp/tmpvxgrjtbo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1t48pwuw/f1.bed -b /tmp/tmp1t48pwuw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp9bo_iv0r/f1.bed -b /tmp/tmp9bo_iv0r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmprbojd_pz/f1.bed -b /tmp/tmprbojd_pz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8cppfh3m/f1.bed -b /tmp/tmp8cppfh3m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp547pzijs/f1.bed -b /tmp/tmp547pzijs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpr3wyf6o9/f1.bed -b /tmp/tmpr3wyf6o9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpg5cr6zy9/f1.bed -b /tmp/tmpg5cr6zy9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp27csyl7n/f1.bed -b /tmp/tmp27csyl7n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1ssn5nhp/f1.bed -b /tmp/tmp1ssn5nhp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmppxt4e8qx/f1.bed -b /tmp/tmppxt4e8qx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpse8in7p7/f1.bed -b /tmp/tmpse8in7p7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzhzw19s1/f1.bed -b /tmp/tmpzhzw19s1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpp17d5_qt/f1.bed -b /tmp/tmpp17d5_qt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgk2ungbi/f1.bed -b /tmp/tmpgk2ungbi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8ut5h0tf/f1.bed -b /tmp/tmp8ut5h0tf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp45tq2h4v/f1.bed -b /tmp/tmp45tq2h4v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbhntm_0o/f1.bed -b /tmp/tmpbhntm_0o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp68vjx9_h/f1.bed -b /tmp/tmp68vjx9_h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpsdciwebe/f1.bed -b /tmp/tmpsdciwebe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpp3u0f1rv/f1.bed -b /tmp/tmpp3u0f1rv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplny1x0j7/f1.bed -b /tmp/tmplny1x0j7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwnyv17qh/f1.bed -b /tmp/tmpwnyv17qh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkz658ys6/f1.bed -b /tmp/tmpkz658ys6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpk6cm8ma2/f1.bed -b /tmp/tmpk6cm8ma2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzi23x5k3/f1.bed -b /tmp/tmpzi23x5k3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpyohn3j6f/f1.bed -b /tmp/tmpyohn3j6f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpx2a0r30c/f1.bed -b /tmp/tmpx2a0r30c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpskaevoqe/f1.bed -b /tmp/tmpskaevoqe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp3dljkcbm/f1.bed -b /tmp/tmp3dljkcbm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp1gu3ejck/f1.bed -b /tmp/tmp1gu3ejck/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphkx0b1ob/f1.bed -b /tmp/tmphkx0b1ob/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfdou5mya/f1.bed -b /tmp/tmpfdou5mya/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpt44rcjt8/f1.bed -b /tmp/tmpt44rcjt8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzfslg6xz/f1.bed -b /tmp/tmpzfslg6xz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpcaqefrlw/f1.bed -b /tmp/tmpcaqefrlw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkvt6fxfn/f1.bed -b /tmp/tmpkvt6fxfn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwrgdrwps/f1.bed -b /tmp/tmpwrgdrwps/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpm_rtq9x3/f1.bed -b /tmp/tmpm_rtq9x3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmphpxqfyvo/f1.bed -b /tmp/tmphpxqfyvo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp81vfh9x9/f1.bed -b /tmp/tmp81vfh9x9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpz3493csc/f1.bed -b /tmp/tmpz3493csc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain15-method_chain15] ___________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False) method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 109 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain64-method_chain64] ___________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same') method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain77-method_chain77] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 155 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ___________ test_three_in_a_row[strandedness_chain70-method_chain70] ___________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 168 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3Q2erSQgcGREYYYGIEkkHIEEkwQESAJhgwAlv8Fkw==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 | (and 220 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges 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'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain25-method_chain25] ___________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ___________ test_three_in_a_row[strandedness_chain42-method_chain42] ___________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:21 E (and 95 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ___________ test_three_in_a_row[strandedness_chain78-method_chain78] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same') method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain96-method_chain96] ___________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain108-method_chain108] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E /usr/lib/python3/dist-packages/pandas/core/common.py:143 E (and 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ______________________ test_nearest[downstream-True-same] ______________________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.End) | ^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 124 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGBEiTBARADi9Axg=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.Start, ocdf.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_ends.values - 1, right_starts.values, right_indexes) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 126 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQEQA4qQMW') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | ~~~~~~~~~~~~~~~~~~~^ | lcol, | ^^^^^ | ...<12 lines>... | check_flags=False, | ^^^^^^^^^^^^^^^^^^ | ) | ^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 471 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpia0p_5hz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpia0p_5hz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpupo58yqq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpupo58yqq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx_r71a38/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx_r71a38/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1249626 1255204 + 0 1 chr1 2204858 2205575 + 0 2 chr1 2204858 2206608 + 0 3 chr1 2204858 2207816 + 0 4 chr1 9295917 9298767 - 0 5 chr12 2204858 2212979 + 0 6 chr14 2204858 2209288 - 0 7 chr16 2204858 2205482 + 0 8 chr5 2204858 2209288 - 0 9 chr6 2204858 2211058 + 0 10 chrY 2204858 2214255 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2204858 | 2207816 | a | 0 | ... | | chr1 | 2204858 | 2206608 | a | 0 | ... | | chr1 | 2204858 | 2205575 | a | 0 | ... | | chr1 | 1249626 | 1255204 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr12 | 2204858 | 2212979 | a | 0 | ... | | chr14 | 2204858 | 2209288 | a | 0 | ... | | chr16 | 2204858 | 2205482 | a | 0 | ... | | chrY | 2204858 | 2214255 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 1249626 1255204 + 0 9 chr16 2204858 2205482 + 0 2 chr1 2204858 2205575 + 0 1 chr1 2204858 2206608 + 0 0 chr1 2204858 2207816 + 0 5 chr5 2204858 2209288 - 0 8 chr14 2204858 2209288 - 0 6 chr6 2204858 2211058 + 0 7 chr12 2204858 2212979 + 0 10 chrY 2204858 2214255 - 0 4 chr1 9295917 9298767 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1249626 1255204 + 0 7 chr16 2204858 2205482 + 0 1 chr1 2204858 2205575 + 0 2 chr1 2204858 2206608 + 0 3 chr1 2204858 2207816 + 0 6 chr14 2204858 2209288 - 0 8 chr5 2204858 2209288 - 0 9 chr6 2204858 2211058 + 0 5 chr12 2204858 2212979 + 0 10 chrY 2204858 2214255 - 0 4 chr1 9295917 9298767 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1249626 1255204 + 0 1 chr1 2204858 2205575 + 0 2 chr1 2204858 2206608 + 0 3 chr1 2204858 2207816 + 0 4 chr1 9295917 9298767 - 0 5 chr12 2204858 2212979 + 0 6 chr14 2204858 2209288 - 0 7 chr16 2204858 2205482 + 0 8 chr5 2204858 2209288 - 0 9 chr6 2204858 2211058 + 0 10 chrY 2204858 2214255 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1249626 1255204 + 0 1 chr1 2204858 2205575 + 0 2 chr1 2204858 2206608 + 0 3 chr1 2204858 2207816 + 0 4 chr1 9295917 9298767 - 0 5 chr12 2204858 2212979 + 0 6 chr14 2204858 2209288 - 0 7 chr16 2204858 2205482 + 0 8 chr5 2204858 2209288 - 0 9 chr6 2204858 2211058 + 0 10 chrY 2204858 2214255 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmxa9e07t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmxa9e07t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6dqxko2k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6dqxko2k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfy7pbd9b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfy7pbd9b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmabs5deo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmabs5deo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr12 1 2 + 0 6 chr14 1 2 + 0 7 chr16 1 2 + 0 8 chr5 1 2 + 0 9 chr6 1 2 + 0 10 chrY 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr12 | 1 | 2 | a | 0 | ... | | chr14 | 1 | 2 | a | 0 | ... | | chr16 | 1 | 2 | a | 0 | ... | | chrY | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr5 1 2 + 0 6 chr6 1 2 + 0 7 chr12 1 2 + 0 8 chr14 1 2 + 0 9 chr16 1 2 + 0 10 chrY 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr12 1 2 + 0 6 chr14 1 2 + 0 7 chr16 1 2 + 0 8 chr5 1 2 + 0 9 chr6 1 2 + 0 10 chrY 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr12 1 2 + 0 6 chr14 1 2 + 0 7 chr16 1 2 + 0 8 chr5 1 2 + 0 9 chr6 1 2 + 0 10 chrY 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr12 1 2 + 0 6 chr14 1 2 + 0 7 chr16 1 2 + 0 8 chr5 1 2 + 0 9 chr6 1 2 + 0 10 chrY 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2iio4z55/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2iio4z55/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr12 1 2 + 0 6 chr14 1 2 + 0 7 chr16 1 2 + 0 8 chr5 1 2 + 0 9 chr6 1 2 + 0 10 chrY 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr12 | 1 | 2 | a | 0 | ... | | chr14 | 1 | 2 | a | 0 | ... | | chr16 | 1 | 2 | a | 0 | ... | | chrY | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr5 1 2 + 0 6 chr6 1 2 + 0 7 chr12 1 2 + 0 8 chr14 1 2 + 0 9 chr16 1 2 + 0 10 chrY 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr12 1 2 + 0 6 chr14 1 2 + 0 7 chr16 1 2 + 0 8 chr5 1 2 + 0 9 chr6 1 2 + 0 10 chrY 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr12 1 2 + 0 6 chr14 1 2 + 0 7 chr16 1 2 + 0 8 chr5 1 2 + 0 9 chr6 1 2 + 0 10 chrY 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr12 1 2 + 0 6 chr14 1 2 + 0 7 chr16 1 2 + 0 8 chr5 1 2 + 0 9 chr6 1 2 + 0 10 chrY 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp76t2u2ny/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp76t2u2ny/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptanq4oar/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptanq4oar/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 518765 521908 + 0 1 chr1 6011734 6011929 + 0 2 chr1 8434592 8441822 - 0 3 chr1 9117674 9122422 - 0 4 chr1 9151189 9160624 - 0 5 chr1 9353780 9363780 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6011734 | 6011929 | a | 0 | ... | | chr1 | 518765 | 521908 | a | 0 | ... | | chr1 | 9353780 | 9363780 | a | 0 | ... | | chr1 | 9117674 | 9122422 | a | 0 | ... | | chr1 | 8434592 | 8441822 | a | 0 | ... | | chr1 | 9151189 | 9160624 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 518765 521908 + 0 0 chr1 6011734 6011929 + 0 4 chr1 8434592 8441822 - 0 3 chr1 9117674 9122422 - 0 5 chr1 9151189 9160624 - 0 2 chr1 9353780 9363780 - 0 df2 Chromosome Start End Strand Distance 0 chr1 518765 521908 + 0 1 chr1 6011734 6011929 + 0 2 chr1 8434592 8441822 - 0 3 chr1 9117674 9122422 - 0 4 chr1 9151189 9160624 - 0 5 chr1 9353780 9363780 - 0 Actual Chromosome Start End Strand Distance 0 chr1 518765 521908 + 0 1 chr1 6011734 6011929 + 0 2 chr1 8434592 8441822 - 0 3 chr1 9117674 9122422 - 0 4 chr1 9151189 9160624 - 0 5 chr1 9353780 9363780 - 0 Expected Chromosome Start End Strand Distance 0 chr1 518765 521908 + 0 1 chr1 6011734 6011929 + 0 2 chr1 8434592 8441822 - 0 3 chr1 9117674 9122422 - 0 4 chr1 9151189 9160624 - 0 5 chr1 9353780 9363780 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9gbt716n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9gbt716n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph9zxnmgo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph9zxnmgo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxq9wx_zh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxq9wx_zh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc89qij0b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc89qij0b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvstzbwzs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvstzbwzs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfekl9ccj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfekl9ccj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvbnoomag/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvbnoomag/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpluev50c3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpluev50c3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb7uodnqk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb7uodnqk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4vwu4tbc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4vwu4tbc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn0y9o7nt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn0y9o7nt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmput4w6k2u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmput4w6k2u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcnkdgu6m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcnkdgu6m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvwerruas/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvwerruas/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcp3gqhnd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcp3gqhnd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpenbkw0tg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpenbkw0tg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8uu_7ngi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8uu_7ngi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp65e8bk_b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp65e8bk_b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplql6vs1u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplql6vs1u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpynfegq03/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpynfegq03/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfj8b4q8y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfj8b4q8y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb_5qa2co/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb_5qa2co/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphkexvk4e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphkexvk4e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph390bxn2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph390bxn2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd28hxl76/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd28hxl76/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxxghye7f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxxghye7f/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppt563cwd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppt563cwd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpldcyd23j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpldcyd23j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk7dvqan7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk7dvqan7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0u05bt7k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0u05bt7k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppml_ccqe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppml_ccqe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfnt08l5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfnt08l5c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvzkoypox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvzkoypox/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfd2x7rzv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfd2x7rzv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphiwszqiy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphiwszqiy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7fkn3tqe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7fkn3tqe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfzq50s6q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfzq50s6q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvjm2eke5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvjm2eke5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphro5pw2y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphro5pw2y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjrx0k_37/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjrx0k_37/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf8iy7e6x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf8iy7e6x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwwo0q8da/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwwo0q8da/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplkq0m5jo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplkq0m5jo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdc_h8i82/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdc_h8i82/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa_urjti0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_urjti0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1m3iugbm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1m3iugbm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmk33qrxl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmk33qrxl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv3b7qoyq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv3b7qoyq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2p561sbl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2p561sbl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp68gp8y1g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp68gp8y1g/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr99k1b9_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr99k1b9_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm20dbixn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm20dbixn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv5o59sox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv5o59sox/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp00991l_u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00991l_u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9sf1fzt3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9sf1fzt3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8je0o2i7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8je0o2i7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgwzpqx_9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgwzpqx_9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnslj3zrf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnslj3zrf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9cgqf88g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9cgqf88g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxt45zyt8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxt45zyt8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd7lc4f8b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd7lc4f8b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnlarvsjf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnlarvsjf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmqcge3xe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmqcge3xe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjy9u6ens/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjy9u6ens/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpft_e4xz1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpft_e4xz1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeaaemu14/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeaaemu14/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_5b_42fp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_5b_42fp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp70ipg4lo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp70ipg4lo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaxho600i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaxho600i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd80j13q4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd80j13q4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqk4dx4wc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqk4dx4wc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqihuhi2u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqihuhi2u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoqxzffn6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoqxzffn6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb2jh5_ws/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb2jh5_ws/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp05of66ne/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp05of66ne/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxr4l88m6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxr4l88m6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqmmp52im/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqmmp52im/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkopjjnik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkopjjnik/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb2o9z_gw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb2o9z_gw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0axx5n80/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0axx5n80/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_3zcs1kj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_3zcs1kj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpku3ohovz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpku3ohovz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpehgghjp9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpehgghjp9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn7yyjf9y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn7yyjf9y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph86d3nu8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph86d3nu8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx9gaboca/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9gaboca/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnh2z1vg5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnh2z1vg5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphoklwwmd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphoklwwmd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaln8gcln/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaln8gcln/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzx24hn75/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzx24hn75/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnfv9xrzf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnfv9xrzf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpctunomdw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpctunomdw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwo4oatll/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwo4oatll/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpez8jzubo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpez8jzubo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprb0j18mq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprb0j18mq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx64io082/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx64io082/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3vwgigbq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3vwgigbq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmuvtefg1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmuvtefg1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqpp3t57h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqpp3t57h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3le0mrwj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3le0mrwj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvo4f5im9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvo4f5im9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphofjwv8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphofjwv8_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv46d3h50/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv46d3h50/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4ffoqhle/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ffoqhle/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvrucl24a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvrucl24a/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvpzzrdv2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvpzzrdv2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5077ll51/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5077ll51/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsvb260bu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsvb260bu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf_vf9o9c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf_vf9o9c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp32fht6t0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp32fht6t0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppvhut34m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppvhut34m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3mixb01d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3mixb01d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfdycv57z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfdycv57z/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl7zp9w9q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl7zp9w9q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5ucaind5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ucaind5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3bkxdys5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3bkxdys5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps9w8wc2r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps9w8wc2r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp559y5ma1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp559y5ma1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2dme0kel/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2dme0kel/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo1xr6fs6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo1xr6fs6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgv684na7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgv684na7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt70zahva/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt70zahva/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_dhgzxkl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_dhgzxkl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp76_2o7fi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp76_2o7fi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7jdgp67m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7jdgp67m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv7g3epes/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv7g3epes/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuu9fyw1g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuu9fyw1g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3yjoigdd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3yjoigdd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj0zrx1kj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj0zrx1kj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfdu5miif/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfdu5miif/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1rnhpjhj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1rnhpjhj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr2 1 2 + 0 2 chr2 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 2 + 0 1 chr2 1 2 + 0 df2 Chromosome Start End Strand Distance 1 chr2 1 2 + 0 2 chr2 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr2 1 2 + 0 1 chr2 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr2 1 2 + 0 1 chr2 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvosri4zo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvosri4zo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn_6f1a0b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn_6f1a0b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzjtltzzz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzjtltzzz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe8ucabv9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8ucabv9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpey3gyboc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpey3gyboc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaz3dr1ez/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaz3dr1ez/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzpvrc94w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzpvrc94w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqopq528n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqopq528n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl6wo03jd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6wo03jd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpczfpv9vj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpczfpv9vj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp080542kr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp080542kr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxf5_jsnj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxf5_jsnj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyus0gyzf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyus0gyzf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7pc_jakk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7pc_jakk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6og5f9iv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6og5f9iv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp21kohn87/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp21kohn87/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2jf2wiss/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2jf2wiss/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7qnoaj4_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qnoaj4_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz1w4s0mv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz1w4s0mv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc3aoqfbx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc3aoqfbx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl982g6qm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl982g6qm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ttnhzj0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ttnhzj0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr7th161f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr7th161f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfqy5f8fy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfqy5f8fy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq9bgegmo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9bgegmo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_zpe20u8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_zpe20u8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_xbdsrtq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_xbdsrtq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplrsnwty1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplrsnwty1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9jxv6o93/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9jxv6o93/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6g3kk7n5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6g3kk7n5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaltv_qr3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaltv_qr3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp50ti0z2n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp50ti0z2n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptou2hkz5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptou2hkz5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpplsarp92/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpplsarp92/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsyb9d_43/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsyb9d_43/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjyu6rt6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjyu6rt6y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmn8d02t_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmn8d02t_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8i3_29tz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8i3_29tz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppxt1enqy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppxt1enqy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl0n7tu_f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0n7tu_f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptcrfnazn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptcrfnazn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwsk42e72/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwsk42e72/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp45b2t68i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp45b2t68i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp17a_m01o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp17a_m01o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp1o9eagj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp1o9eagj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9c80ua0q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9c80ua0q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps19fhadn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps19fhadn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdbqwa8t8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdbqwa8t8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw6zyvkoy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw6zyvkoy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgm4sgh5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgm4sgh5d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpndpvg_58/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpndpvg_58/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp183uea64/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp183uea64/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2uz8xx05/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2uz8xx05/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkx4oi1pt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkx4oi1pt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppdzcfra7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppdzcfra7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp30e1rfpz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp30e1rfpz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwwmmc44m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwwmmc44m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8khvlxws/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8khvlxws/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxuahhx0i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxuahhx0i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv6ewxbuo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv6ewxbuo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphmi4m05s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphmi4m05s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpco1152wc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpco1152wc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk_xm3ac2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_xm3ac2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphj2vwvk2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphj2vwvk2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpucgccg6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpucgccg6y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqoerpju2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqoerpju2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5ts05ris/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ts05ris/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7d_5fjhd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7d_5fjhd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy0z54tzd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy0z54tzd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjio7r4y2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjio7r4y2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeb6m8k08/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeb6m8k08/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_s9btvsc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_s9btvsc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgo0ysb14/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgo0ysb14/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpesg7vfso/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpesg7vfso/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv_5hqlz0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv_5hqlz0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdmrinpdl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdmrinpdl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1i46bzkp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1i46bzkp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9qbcuydu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qbcuydu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps4w4i7dw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps4w4i7dw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsd36m7l4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsd36m7l4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw_b3_ky6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw_b3_ky6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpitd2xaqu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpitd2xaqu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiztetmz3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiztetmz3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpft8wbcb8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpft8wbcb8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg6txmcbi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg6txmcbi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnl3bgf3_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnl3bgf3_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpijsr5ken/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpijsr5ken/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp11p_bklt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp11p_bklt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa4y6_qda/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa4y6_qda/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd1gpek4z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd1gpek4z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv3dll5h8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv3dll5h8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw_fwcz0y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw_fwcz0y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_q92b4v4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_q92b4v4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpubqkbvyo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpubqkbvyo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz0k6wk_r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz0k6wk_r/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz6jr0ns7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz6jr0ns7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg_4inn5o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg_4inn5o/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfzcyyf0l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfzcyyf0l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2c33dkoj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2c33dkoj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy9qf_vay/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy9qf_vay/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy_y27qx7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy_y27qx7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0lvbg4nu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0lvbg4nu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgh8gwvn1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgh8gwvn1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_3f93idp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_3f93idp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzoqm3ozi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzoqm3ozi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphuwqox2i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphuwqox2i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7xk3i0ce/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7xk3i0ce/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps5y2xt4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps5y2xt4v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppztmyw9u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppztmyw9u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp57vabrw8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp57vabrw8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvzmwmjah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvzmwmjah/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprg0e752_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprg0e752_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 2 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfw498vwr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfw498vwr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp61d0cwbg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp61d0cwbg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbidkhruz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbidkhruz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprz_cfs3d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprz_cfs3d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl35_zqg5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl35_zqg5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 2 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9z2pw_i8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9z2pw_i8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5fdece3_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5fdece3_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp05obtucf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp05obtucf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcei6el03/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcei6el03/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsl81etgf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsl81etgf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo02f8yzb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo02f8yzb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkupmfame/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkupmfame/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpba_jmje3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpba_jmje3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqd4zd00m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqd4zd00m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm_34o1wd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm_34o1wd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjniluy5o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjniluy5o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzk498r2b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzk498r2b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc13x3atc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc13x3atc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcrg0_c1_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcrg0_c1_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuxv7wpqs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuxv7wpqs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_ucp8ql5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ucp8ql5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgtz969a8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgtz969a8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn25cyvgd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn25cyvgd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc5hcusmg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc5hcusmg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8qfeeu9d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8qfeeu9d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyvuhn5es/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyvuhn5es/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbo_ox0ai/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbo_ox0ai/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwhd61xg_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwhd61xg_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbn62deid/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbn62deid/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp49d9iybz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp49d9iybz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdt7t4_v7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdt7t4_v7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdiab1bs_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdiab1bs_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvtq8x1ym/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtq8x1ym/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp42wicflu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp42wicflu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa8o249wf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa8o249wf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7fpeg7dm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7fpeg7dm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq9p9rnnh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9p9rnnh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfbekib95/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfbekib95/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd04_1t18/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd04_1t18/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbukqr0c3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbukqr0c3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4t_h97sz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4t_h97sz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsmpph6h3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsmpph6h3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqwf1w_r9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqwf1w_r9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphihdku0n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphihdku0n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbddu7lic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbddu7lic/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg7ta0ucl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7ta0ucl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr0dvbq2o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr0dvbq2o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5hbggzm0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5hbggzm0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx0ct3bu_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx0ct3bu_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk0e43j2c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk0e43j2c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4czgwbir/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4czgwbir/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpujw94hpp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpujw94hpp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu7sqfrb6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu7sqfrb6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx3ssi_th/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3ssi_th/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvbwmo6q_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvbwmo6q_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplq0oowq_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplq0oowq_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpth0k4cx3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpth0k4cx3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7mz2dtqc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7mz2dtqc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp8fhvruc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp8fhvruc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ot98kkh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ot98kkh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp308cz1fy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp308cz1fy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsfmt4v5n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsfmt4v5n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvrel3cgs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvrel3cgs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqr3eq0sv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqr3eq0sv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph9rqpvvy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph9rqpvvy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_5epxok0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_5epxok0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgughxew_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgughxew_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxr4wa0oo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxr4wa0oo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj9s1na_g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj9s1na_g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9t9ep66l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9t9ep66l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw1gxkrxt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw1gxkrxt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4n5wzxb_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4n5wzxb_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 2 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjmc_p1me/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjmc_p1me/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_01zr2e4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_01zr2e4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1xxoxsb0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1xxoxsb0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjhz7hhxz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjhz7hhxz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp056zr0b6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp056zr0b6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpig11_rg7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpig11_rg7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwmkf_lvh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwmkf_lvh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpscqv31ln/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpscqv31ln/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2e38wfy_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2e38wfy_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8c_db6x7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8c_db6x7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjdt_03yf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjdt_03yf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj8t7qseh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj8t7qseh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz2wms8_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz2wms8_e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphh38skth/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphh38skth/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc6dhgvie/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc6dhgvie/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp01n_0zfc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp01n_0zfc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4rnjt8kf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4rnjt8kf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuywl1v2q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuywl1v2q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjo2eiir4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjo2eiir4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx3mj8f15/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3mj8f15/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp37lve_bu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp37lve_bu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpylse8tjg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpylse8tjg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6i0zwlh1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6i0zwlh1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpodas9eno/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpodas9eno/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpreo82g28/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpreo82g28/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp66mz2ujw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp66mz2ujw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpspiu2uao/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpspiu2uao/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpccpqxrui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpccpqxrui/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq259726q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq259726q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl1vew_o1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl1vew_o1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg47g00eh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg47g00eh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp811e5hwq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp811e5hwq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsljcuh4m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsljcuh4m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2crxeiib/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2crxeiib/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp426oxh7d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp426oxh7d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphbqgi_it/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphbqgi_it/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn6s_nxqd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn6s_nxqd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm1nnc0ik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm1nnc0ik/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpugwu8lak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpugwu8lak/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu7cc4fdg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu7cc4fdg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplu_38y3o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplu_38y3o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwkfx2sw2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwkfx2sw2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1ymabefu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ymabefu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph73ao9qf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph73ao9qf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnut55xw4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnut55xw4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdw6xjjvk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdw6xjjvk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprvs6svdb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprvs6svdb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ________________ test_k_nearest[downstream-False-opposite-last] ________________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1e.values, d2s.values, d1e.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=False, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjRRRgBOKMDFg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1s.values, d2e.values, d1s.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=False, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGMEijDDEAAAx1ALW') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzw37kp79/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzw37kp79/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoypt80je/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoypt80je/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5fzu425h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5fzu425h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpra2m2f7s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpra2m2f7s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyhlu3d5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyhlu3d5d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa6jcddxk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa6jcddxk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn516wddk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn516wddk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4lxxj7zg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4lxxj7zg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8yku2wzd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8yku2wzd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeqa5o5li/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeqa5o5li/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8b2zy131/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8b2zy131/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvmamdpkn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvmamdpkn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpepgwmanw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpepgwmanw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7jts8bw_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7jts8bw_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxt218098/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxt218098/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7_qmg17m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7_qmg17m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdyd2y_wk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdyd2y_wk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp486px1r5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp486px1r5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmput_hfojq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmput_hfojq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7n7v_k4g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7n7v_k4g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsx9j0b3s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsx9j0b3s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnp3uoeeg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnp3uoeeg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpygta6jl0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpygta6jl0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo9rrorh4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo9rrorh4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyljkq9wx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyljkq9wx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn1tlgwwr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn1tlgwwr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfbtw3bo4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfbtw3bo4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnhluf7wz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnhluf7wz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu5xk5j77/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu5xk5j77/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp40usxk1w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp40usxk1w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoxhri2pc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoxhri2pc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm14u29qa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm14u29qa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9ztzizxc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ztzizxc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm_eudr1x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm_eudr1x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbqzigihl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbqzigihl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvrkxrx1n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvrkxrx1n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi_9g47vf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi_9g47vf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp89dlzoh1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp89dlzoh1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj9x6pwl1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj9x6pwl1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv2t4j7er/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv2t4j7er/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyscudx2b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyscudx2b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4rs0snro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4rs0snro/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt3c903lz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt3c903lz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp93pp5z6b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp93pp5z6b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg1d0cp8g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg1d0cp8g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp84f1zpfa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp84f1zpfa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsoy7puq6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsoy7puq6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp23zea6km/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp23zea6km/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb56f3tks/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb56f3tks/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpos6uab7z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpos6uab7z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps7tygjlf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps7tygjlf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwquzwemf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwquzwemf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplzif5qqz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplzif5qqz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4bmrcac6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4bmrcac6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4o_72w8d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4o_72w8d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp18u4np79/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp18u4np79/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbkoxq22i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbkoxq22i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpshab41gn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpshab41gn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfkwgl2v2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfkwgl2v2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgg2o0be_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgg2o0be_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpitsb_epw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpitsb_epw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpacp0k4l_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpacp0k4l_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0y8gsb5o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0y8gsb5o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoux41i6d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoux41i6d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkswl3g0b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkswl3g0b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0x1uyrf4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0x1uyrf4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgy8_d4q6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgy8_d4q6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoot2nxap/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoot2nxap/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa228tcwo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa228tcwo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgzdoc4wv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgzdoc4wv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7qtgo1aq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qtgo1aq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp87i6z8_q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp87i6z8_q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpidunrz_7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpidunrz_7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa9w4q7xp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa9w4q7xp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5eza4f2j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5eza4f2j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmperpxvj33/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmperpxvj33/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8ncuatyf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ncuatyf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt90shehn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt90shehn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq7dfvby7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq7dfvby7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcu45walg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcu45walg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe1sxv8st/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe1sxv8st/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp19xzhjfu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp19xzhjfu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6pywpmso/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6pywpmso/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk8d4nhfu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk8d4nhfu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprn3l_knw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprn3l_knw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbqyr0t7e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbqyr0t7e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeawrnu0i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeawrnu0i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuetkfmyh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuetkfmyh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcg_7kjzw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcg_7kjzw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8nihmbo2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8nihmbo2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp97ru8se9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp97ru8se9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3qfzhjaf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3qfzhjaf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprdn5z_j9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprdn5z_j9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpotr9c9ce/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpotr9c9ce/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp48d4ifst/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp48d4ifst/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnqybx_vu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnqybx_vu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6tv_sad2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6tv_sad2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmjlwitkv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmjlwitkv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw7xqk8cx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw7xqk8cx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoo21yjzd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoo21yjzd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_t6zlcub/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_t6zlcub/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpel3itn0v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpel3itn0v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpquo5tf3v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpquo5tf3v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3ly028_y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ly028_y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphyyza_vv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphyyza_vv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5pblpi8d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5pblpi8d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpybai5hxc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpybai5hxc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmrz5ih9b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmrz5ih9b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu913woxh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu913woxh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk5tcxueq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk5tcxueq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0a5lnduu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0a5lnduu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnur_q1sb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnur_q1sb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdmof48e3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdmof48e3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_kpomgm7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_kpomgm7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd1c499b6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd1c499b6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprgi3ycsm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprgi3ycsm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpke0b_oa8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpke0b_oa8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdl3bc2qg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdl3bc2qg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1q1ykkfa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1q1ykkfa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7rfpm_c1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7rfpm_c1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfub3c03p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfub3c03p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjo9ikep1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjo9ikep1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz96s5kq_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz96s5kq_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp252vzf3i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp252vzf3i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnu3nwfc5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnu3nwfc5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3ctjrxq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ctjrxq2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpie430ujt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpie430ujt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3dycl675/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3dycl675/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5dv2x51x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5dv2x51x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvdxxcmh8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvdxxcmh8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkzwuk_xm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkzwuk_xm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpedjr7z6m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpedjr7z6m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj0h_7p4j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj0h_7p4j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5ia2gjy6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ia2gjy6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1j3arqmq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1j3arqmq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv4l8tjkw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv4l8tjkw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjbifclit/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjbifclit/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_jzx9xo9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_jzx9xo9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4xgusvns/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4xgusvns/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8e7e3nrj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8e7e3nrj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4y9rqmf8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4y9rqmf8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplmvwxzle/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplmvwxzle/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgjk6zqsv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgjk6zqsv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpleavcfq7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpleavcfq7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeqo4w805/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeqo4w805/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpct3id4mq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpct3id4mq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppo3zy1a0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppo3zy1a0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcj___q_b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcj___q_b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkfe3q7jk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkfe3q7jk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeyv8qte2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeyv8qte2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4bczqpld/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4bczqpld/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppysdknn9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppysdknn9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptanoc8uo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptanoc8uo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc9z_41s5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc9z_41s5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4r1f2r1u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4r1f2r1u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_p3rft_b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_p3rft_b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplewc0qto/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplewc0qto/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl2_bislc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl2_bislc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbv9snoom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbv9snoom/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj2jqqrzg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj2jqqrzg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmlcvs9fg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmlcvs9fg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpos7tg7pr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpos7tg7pr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb86p_mt0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb86p_mt0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptix1_8st/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptix1_8st/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw4ud4ep9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw4ud4ep9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz13bw64j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz13bw64j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyrphwb9v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyrphwb9v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaywxjh3s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaywxjh3s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyoep4vzi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyoep4vzi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps45lq1hf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps45lq1hf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr4s8d1h_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr4s8d1h_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbau1drb8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbau1drb8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3ng0covy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ng0covy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3xlpzktn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3xlpzktn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp68qo8zr2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp68qo8zr2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjf72y2jn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjf72y2jn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv2d_u0qy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv2d_u0qy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy4pitvwb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy4pitvwb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxog0h4c_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxog0h4c_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1og9zszo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1og9zszo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphv_g5kmt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphv_g5kmt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsiyjdvik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsiyjdvik/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppfb5uhsn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppfb5uhsn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiqw232ki/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiqw232ki/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6_awi8kf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6_awi8kf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8qt1rs0n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8qt1rs0n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm7pulgqq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm7pulgqq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp_lxo8tx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_lxo8tx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphq5aij7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphq5aij7q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk2t0izbj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk2t0izbj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx4ggtydl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx4ggtydl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplwzlma9s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplwzlma9s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppgaw7ijz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppgaw7ijz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpld97s1f3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpld97s1f3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2zf_h0lq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2zf_h0lq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoauqsjmv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoauqsjmv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyhgdyyom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyhgdyyom/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqk5dlzwm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqk5dlzwm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmko8og5_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmko8og5_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0hzf1xf7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0hzf1xf7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7f7o52p0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7f7o52p0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaftyn_76/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaftyn_76/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3ersyrjy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ersyrjy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc8p018ct/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc8p018ct/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9lugsv3b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9lugsv3b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbc1tqkgn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbc1tqkgn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4x3ffscg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4x3ffscg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgcxovmw1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgcxovmw1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvzqt3zf9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvzqt3zf9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpns_lf2ny/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpns_lf2ny/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq5b4fs3x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq5b4fs3x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnzb4aa9q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnzb4aa9q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpffovk3cx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpffovk3cx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp6xvujay/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp6xvujay/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy95p5ooh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy95p5ooh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnggwuylt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnggwuylt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp10pjgo6l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp10pjgo6l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg_h6loj2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg_h6loj2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp82tfhik5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp82tfhik5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsupbe7ba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsupbe7ba/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbr1p2r8u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbr1p2r8u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqs5wycru/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqs5wycru/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9m72jgbm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9m72jgbm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4etzfvzn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4etzfvzn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphip86wbn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphip86wbn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp77y3yg8z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp77y3yg8z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjohd7uyt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjohd7uyt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp97y8gyek/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp97y8gyek/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7tzs67c5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7tzs67c5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpspxamp0q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpspxamp0q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps6bo2_or/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps6bo2_or/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbxw8fuec/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbxw8fuec/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3riq5rvc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3riq5rvc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm3y3pr3q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm3y3pr3q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6odu0e5b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6odu0e5b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6k70qzoz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6k70qzoz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw_mr8mbs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw_mr8mbs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp84jywb4m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp84jywb4m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd_y03uy6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd_y03uy6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9jb12_ua/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9jb12_ua/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6xcaecal/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6xcaecal/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfonv82hs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfonv82hs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpynfp4zi5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpynfp4zi5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcfz7wn6k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcfz7wn6k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa02pjc1v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa02pjc1v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwb_xrbjd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwb_xrbjd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpunk1q4bq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpunk1q4bq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2v0bmkic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2v0bmkic/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwsp_73jb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwsp_73jb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu21jc_4o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu21jc_4o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn1x98xdq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn1x98xdq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp09kvoc18/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp09kvoc18/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk5_k1rr_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk5_k1rr_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpose1iaqr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpose1iaqr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6swo2i97/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6swo2i97/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcbt9v5jp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcbt9v5jp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpph7csf77/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpph7csf77/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxtvg0x0o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxtvg0x0o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzwqwtl2e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzwqwtl2e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxhs2qv_j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxhs2qv_j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp204audn9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp204audn9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkyo05zwy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkyo05zwy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj2ryt60s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj2ryt60s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmzofn8ch/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmzofn8ch/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmper6ff_eh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmper6ff_eh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbrqfjh1c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbrqfjh1c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9mrzu515/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9mrzu515/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0twlps_p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0twlps_p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3avfq549/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3avfq549/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1sw8b5tu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1sw8b5tu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpii0k9jyu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpii0k9jyu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpttmwotik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpttmwotik/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6wpz2t14/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6wpz2t14/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpra4kcins/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpra4kcins/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdgqf6bhv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdgqf6bhv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl8tn9v0p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl8tn9v0p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3yvr41x8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3yvr41x8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8ja00pgq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ja00pgq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps11k8kem/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps11k8kem/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfo6kjgpn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfo6kjgpn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpshy3a533/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpshy3a533/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjsppd2_0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjsppd2_0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkasligqc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkasligqc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzyhzxqw2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzyhzxqw2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp46s34eh1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp46s34eh1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq2bwoj8a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq2bwoj8a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8kggvjpd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8kggvjpd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9q1qwj3i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9q1qwj3i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvfxmxd_5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvfxmxd_5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp44nd65zh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp44nd65zh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpizg89txl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpizg89txl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjowvc0su/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjowvc0su/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeao3s410/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeao3s410/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuwep1e44/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuwep1e44/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpebyp7zxr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpebyp7zxr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyahsc8sf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyahsc8sf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpii08p30b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpii08p30b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcx0adje4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcx0adje4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz62m7cut/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz62m7cut/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0mlwym2s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0mlwym2s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpegftclp_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpegftclp_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmrsg1au5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmrsg1au5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1g37m5ne/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1g37m5ne/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpimh5k0qm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpimh5k0qm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp289l7m74/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp289l7m74/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1uy91agg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1uy91agg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxj63xcr4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxj63xcr4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn_84b9qy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn_84b9qy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgcgot6n4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgcgot6n4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzxdbc3m9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzxdbc3m9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr0qfi6z1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr0qfi6z1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6qt64nm7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6qt64nm7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_f5x7son/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_f5x7son/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1gf1tf19/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1gf1tf19/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpindw0u7d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpindw0u7d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7yqd7j52/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7yqd7j52/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpayz9m2q1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpayz9m2q1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi23fm5lr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi23fm5lr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7w3utqhv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7w3utqhv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpalw1elc2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpalw1elc2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0tnwdbko/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0tnwdbko/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxzy36nwj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxzy36nwj/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr4 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________________________ test_subtraction[False] ____________________________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", ["same", "opposite", False]) # tests/test_binary.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:308: in test_subtraction result = gr.subtract(gr2, strandedness=strandedness) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_subtraction( E # The test always failed when commented parts were varied together. E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1nt70wml/f1.bed -b /tmp/tmp1nt70wml/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpc20uuj26/f1.bed -b /tmp/tmpc20uuj26/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpcpq8o9gw/f1.bed -b /tmp/tmpcpq8o9gw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp8ae7tgk8/f1.bed -b /tmp/tmp8ae7tgk8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2461r49r/f1.bed -b /tmp/tmp2461r49r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpsqanf_f3/f1.bed -b /tmp/tmpsqanf_f3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1ole6abo/f1.bed -b /tmp/tmp1ole6abo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpfr_pth0r/f1.bed -b /tmp/tmpfr_pth0r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpa83ybmu1/f1.bed -b /tmp/tmpa83ybmu1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjmh6jgp3/f1.bed -b /tmp/tmpjmh6jgp3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpc2tyqxij/f1.bed -b /tmp/tmpc2tyqxij/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmptdpjryoi/f1.bed -b /tmp/tmptdpjryoi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpuonlozgh/f1.bed -b /tmp/tmpuonlozgh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpurbguuiv/f1.bed -b /tmp/tmpurbguuiv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpt7v8nnts/f1.bed -b /tmp/tmpt7v8nnts/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgjg1adve/f1.bed -b /tmp/tmpgjg1adve/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpes58t1l_/f1.bed -b /tmp/tmpes58t1l_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmppcf5r7a2/f1.bed -b /tmp/tmppcf5r7a2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpatqxv07w/f1.bed -b /tmp/tmpatqxv07w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpx6b6gc0k/f1.bed -b /tmp/tmpx6b6gc0k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5hvfmgfo/f1.bed -b /tmp/tmp5hvfmgfo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdywkvwzt/f1.bed -b /tmp/tmpdywkvwzt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpz_rnecgi/f1.bed -b /tmp/tmpz_rnecgi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwnqf6fke/f1.bed -b /tmp/tmpwnqf6fke/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp696azxr2/f1.bed -b /tmp/tmp696azxr2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp0tqexk_q/f1.bed -b /tmp/tmp0tqexk_q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpy7zx413u/f1.bed -b /tmp/tmpy7zx413u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp43q5es9n/f1.bed -b /tmp/tmp43q5es9n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbqlkx9gs/f1.bed -b /tmp/tmpbqlkx9gs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmhuqzxoq/f1.bed -b /tmp/tmpmhuqzxoq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6_59w62_/f1.bed -b /tmp/tmp6_59w62_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2p3d4_jo/f1.bed -b /tmp/tmp2p3d4_jo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp8iui2o_q/f1.bed -b /tmp/tmp8iui2o_q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpa_9b03wh/f1.bed -b /tmp/tmpa_9b03wh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpg2m3g5ey/f1.bed -b /tmp/tmpg2m3g5ey/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5jdsr_t0/f1.bed -b /tmp/tmp5jdsr_t0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpx6j5h0ft/f1.bed -b /tmp/tmpx6j5h0ft/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprrw47pmk/f1.bed -b /tmp/tmprrw47pmk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpu5hj1n94/f1.bed -b /tmp/tmpu5hj1n94/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjc36h19i/f1.bed -b /tmp/tmpjc36h19i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp98ycyris/f1.bed -b /tmp/tmp98ycyris/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp0zr_avbn/f1.bed -b /tmp/tmp0zr_avbn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpr7rwdp8i/f1.bed -b /tmp/tmpr7rwdp8i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpvv62seo5/f1.bed -b /tmp/tmpvv62seo5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3dtcxkk8/f1.bed -b /tmp/tmp3dtcxkk8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpvzdii5b6/f1.bed -b /tmp/tmpvzdii5b6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprn4mnbyu/f1.bed -b /tmp/tmprn4mnbyu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqs7_a2v4/f1.bed -b /tmp/tmpqs7_a2v4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpo0vjrs2f/f1.bed -b /tmp/tmpo0vjrs2f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpsuqax81v/f1.bed -b /tmp/tmpsuqax81v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpexhgetbw/f1.bed -b /tmp/tmpexhgetbw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpcuyoshpd/f1.bed -b /tmp/tmpcuyoshpd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwtbxicub/f1.bed -b /tmp/tmpwtbxicub/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpn89_nzxb/f1.bed -b /tmp/tmpn89_nzxb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9heka20d/f1.bed -b /tmp/tmp9heka20d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpofp3dgbr/f1.bed -b /tmp/tmpofp3dgbr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp58r0i3cg/f1.bed -b /tmp/tmp58r0i3cg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp33yyabz2/f1.bed -b /tmp/tmp33yyabz2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmkmj_4x9/f1.bed -b /tmp/tmpmkmj_4x9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqj2mf67i/f1.bed -b /tmp/tmpqj2mf67i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpb4i6kjgp/f1.bed -b /tmp/tmpb4i6kjgp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp59qarc0r/f1.bed -b /tmp/tmp59qarc0r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmstqk08x/f1.bed -b /tmp/tmpmstqk08x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpu1kydpr6/f1.bed -b /tmp/tmpu1kydpr6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpyvuzhp1c/f1.bed -b /tmp/tmpyvuzhp1c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpvb1mdjo3/f1.bed -b /tmp/tmpvb1mdjo3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2gixyg3z/f1.bed -b /tmp/tmp2gixyg3z/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqqw2hvb9/f1.bed -b /tmp/tmpqqw2hvb9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3er35tg7/f1.bed -b /tmp/tmp3er35tg7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7o7nk9ep/f1.bed -b /tmp/tmp7o7nk9ep/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpvomizf_c/f1.bed -b /tmp/tmpvomizf_c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9yvu43y1/f1.bed -b /tmp/tmp9yvu43y1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmphzhs87mc/f1.bed -b /tmp/tmphzhs87mc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5tmacc7c/f1.bed -b /tmp/tmp5tmacc7c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5sm924q8/f1.bed -b /tmp/tmp5sm924q8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdotwipkc/f1.bed -b /tmp/tmpdotwipkc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpcpuscqlh/f1.bed -b /tmp/tmpcpuscqlh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpyc3vfsfm/f1.bed -b /tmp/tmpyc3vfsfm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7zp_c5xs/f1.bed -b /tmp/tmp7zp_c5xs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpweoo1gcl/f1.bed -b /tmp/tmpweoo1gcl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpvkv137n4/f1.bed -b /tmp/tmpvkv137n4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpxuby_vt4/f1.bed -b /tmp/tmpxuby_vt4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdory1n9o/f1.bed -b /tmp/tmpdory1n9o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp4ienda01/f1.bed -b /tmp/tmp4ienda01/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9dyac4t9/f1.bed -b /tmp/tmp9dyac4t9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpac7i3acb/f1.bed -b /tmp/tmpac7i3acb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmsbsdsgh/f1.bed -b /tmp/tmpmsbsdsgh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpcwqpfsu_/f1.bed -b /tmp/tmpcwqpfsu_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpozfzljln/f1.bed -b /tmp/tmpozfzljln/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9rhwy8wm/f1.bed -b /tmp/tmp9rhwy8wm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpt2rbcfz2/f1.bed -b /tmp/tmpt2rbcfz2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpf62aw1bt/f1.bed -b /tmp/tmpf62aw1bt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpoitt8yv7/f1.bed -b /tmp/tmpoitt8yv7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp28quk4n9/f1.bed -b /tmp/tmp28quk4n9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpn5lv9m6v/f1.bed -b /tmp/tmpn5lv9m6v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpi18oa7sr/f1.bed -b /tmp/tmpi18oa7sr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmppjum3xvw/f1.bed -b /tmp/tmppjum3xvw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2a8vf257/f1.bed -b /tmp/tmp2a8vf257/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpd2s7pxv6/f1.bed -b /tmp/tmpd2s7pxv6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgnqgcb60/f1.bed -b /tmp/tmpgnqgcb60/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpvg0bbcjq/f1.bed -b /tmp/tmpvg0bbcjq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwmgjspj4/f1.bed -b /tmp/tmpwmgjspj4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpheqgnehw/f1.bed -b /tmp/tmpheqgnehw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1ejybrb2/f1.bed -b /tmp/tmp1ejybrb2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpm6lhrcnr/f1.bed -b /tmp/tmpm6lhrcnr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmmul9nw6/f1.bed -b /tmp/tmpmmul9nw6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmppv3g3x69/f1.bed -b /tmp/tmppv3g3x69/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_u5xs_cx/f1.bed -b /tmp/tmp_u5xs_cx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7siz6sco/f1.bed -b /tmp/tmp7siz6sco/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpw7ykwus6/f1.bed -b /tmp/tmpw7ykwus6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjuejzu1y/f1.bed -b /tmp/tmpjuejzu1y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6rtgrefx/f1.bed -b /tmp/tmp6rtgrefx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpq5_wvzek/f1.bed -b /tmp/tmpq5_wvzek/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1gsm2bwf/f1.bed -b /tmp/tmp1gsm2bwf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpuowkuo5o/f1.bed -b /tmp/tmpuowkuo5o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmppd_lr39l/f1.bed -b /tmp/tmppd_lr39l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5e4_qsn2/f1.bed -b /tmp/tmp5e4_qsn2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwua31ac0/f1.bed -b /tmp/tmpwua31ac0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmph7pixr9n/f1.bed -b /tmp/tmph7pixr9n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpsz2kzuld/f1.bed -b /tmp/tmpsz2kzuld/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpruh32e5n/f1.bed -b /tmp/tmpruh32e5n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpy1v9y176/f1.bed -b /tmp/tmpy1v9y176/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpyq5tmn52/f1.bed -b /tmp/tmpyq5tmn52/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdzjzieoy/f1.bed -b /tmp/tmpdzjzieoy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpcpapyemm/f1.bed -b /tmp/tmpcpapyemm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpyjra866n/f1.bed -b /tmp/tmpyjra866n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpkg9rpwuh/f1.bed -b /tmp/tmpkg9rpwuh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpw9bk3o5a/f1.bed -b /tmp/tmpw9bk3o5a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpapfapcdm/f1.bed -b /tmp/tmpapfapcdm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpj3rr84yj/f1.bed -b /tmp/tmpj3rr84yj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpcfab48un/f1.bed -b /tmp/tmpcfab48un/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9gq6zto3/f1.bed -b /tmp/tmp9gq6zto3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6n6mzaqz/f1.bed -b /tmp/tmp6n6mzaqz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp40_m4z_3/f1.bed -b /tmp/tmp40_m4z_3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9koesj5s/f1.bed -b /tmp/tmp9koesj5s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp85g9pz0i/f1.bed -b /tmp/tmp85g9pz0i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgl2axa_a/f1.bed -b /tmp/tmpgl2axa_a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp4u7o65dj/f1.bed -b /tmp/tmp4u7o65dj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpyq7451t8/f1.bed -b /tmp/tmpyq7451t8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp4kx8oaw6/f1.bed -b /tmp/tmp4kx8oaw6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp74t37_is/f1.bed -b /tmp/tmp74t37_is/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_xfkjs1n/f1.bed -b /tmp/tmp_xfkjs1n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpph0ek_of/f1.bed -b /tmp/tmpph0ek_of/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_6wvmd0p/f1.bed -b /tmp/tmp_6wvmd0p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp0vj3fmco/f1.bed -b /tmp/tmp0vj3fmco/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmps2yti_1_/f1.bed -b /tmp/tmps2yti_1_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9ddaf35h/f1.bed -b /tmp/tmp9ddaf35h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjur39iqt/f1.bed -b /tmp/tmpjur39iqt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpsrlxh8lh/f1.bed -b /tmp/tmpsrlxh8lh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9bev9n1i/f1.bed -b /tmp/tmp9bev9n1i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdgdxh6va/f1.bed -b /tmp/tmpdgdxh6va/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpsf43a3z0/f1.bed -b /tmp/tmpsf43a3z0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp43a54zv6/f1.bed -b /tmp/tmp43a54zv6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwgn2pcmo/f1.bed -b /tmp/tmpwgn2pcmo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_w_bevcl/f1.bed -b /tmp/tmp_w_bevcl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6wl62pnx/f1.bed -b /tmp/tmp6wl62pnx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp8yqki21c/f1.bed -b /tmp/tmp8yqki21c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp0egbv6p4/f1.bed -b /tmp/tmp0egbv6p4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwtsv37tx/f1.bed -b /tmp/tmpwtsv37tx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpd8nla24s/f1.bed -b /tmp/tmpd8nla24s/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmph3j0lscn/f1.bed -b /tmp/tmph3j0lscn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5cds20h2/f1.bed -b /tmp/tmp5cds20h2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpptm2vgir/f1.bed -b /tmp/tmpptm2vgir/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpfb8_thr5/f1.bed -b /tmp/tmpfb8_thr5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpzp9erbaa/f1.bed -b /tmp/tmpzp9erbaa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprepmekd6/f1.bed -b /tmp/tmprepmekd6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpl08xetg8/f1.bed -b /tmp/tmpl08xetg8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpfgq4pn06/f1.bed -b /tmp/tmpfgq4pn06/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpaqtx3fwe/f1.bed -b /tmp/tmpaqtx3fwe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpucc9w79m/f1.bed -b /tmp/tmpucc9w79m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmppbz9salf/f1.bed -b /tmp/tmppbz9salf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmppy2f7iug/f1.bed -b /tmp/tmppy2f7iug/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpzls03crp/f1.bed -b /tmp/tmpzls03crp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp8edo88y6/f1.bed -b /tmp/tmp8edo88y6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpidv2j6ne/f1.bed -b /tmp/tmpidv2j6ne/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqtsvlda0/f1.bed -b /tmp/tmpqtsvlda0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpg1utc194/f1.bed -b /tmp/tmpg1utc194/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpoeuknq2f/f1.bed -b /tmp/tmpoeuknq2f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmph_qy9k8a/f1.bed -b /tmp/tmph_qy9k8a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp4yplj0d9/f1.bed -b /tmp/tmp4yplj0d9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpoft4u_qb/f1.bed -b /tmp/tmpoft4u_qb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpyhelde7a/f1.bed -b /tmp/tmpyhelde7a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpp5l2xv4r/f1.bed -b /tmp/tmpp5l2xv4r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpz29ou9nb/f1.bed -b /tmp/tmpz29ou9nb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp4c2poqmd/f1.bed -b /tmp/tmp4c2poqmd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnxwym7__/f1.bed -b /tmp/tmpnxwym7__/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpx58foh2m/f1.bed -b /tmp/tmpx58foh2m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5hxt15fq/f1.bed -b /tmp/tmp5hxt15fq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp25extdx7/f1.bed -b /tmp/tmp25extdx7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpvhyl0mhc/f1.bed -b /tmp/tmpvhyl0mhc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_amoqvzg/f1.bed -b /tmp/tmp_amoqvzg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp10nm5a03/f1.bed -b /tmp/tmp10nm5a03/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpi8fajk6i/f1.bed -b /tmp/tmpi8fajk6i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpcnm87tfk/f1.bed -b /tmp/tmpcnm87tfk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqzi34628/f1.bed -b /tmp/tmpqzi34628/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpoi44z9v7/f1.bed -b /tmp/tmpoi44z9v7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp0l_9smlh/f1.bed -b /tmp/tmp0l_9smlh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp42e3jge1/f1.bed -b /tmp/tmp42e3jge1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmlmuc4re/f1.bed -b /tmp/tmpmlmuc4re/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpn1oeo7_1/f1.bed -b /tmp/tmpn1oeo7_1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp968hfj32/f1.bed -b /tmp/tmp968hfj32/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6z1kau3g/f1.bed -b /tmp/tmp6z1kau3g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_qybzh25/f1.bed -b /tmp/tmp_qybzh25/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpsz797y4m/f1.bed -b /tmp/tmpsz797y4m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgb68_wko/f1.bed -b /tmp/tmpgb68_wko/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1p7hmsix/f1.bed -b /tmp/tmp1p7hmsix/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqt9v7b3m/f1.bed -b /tmp/tmpqt9v7b3m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpfagr4pie/f1.bed -b /tmp/tmpfagr4pie/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpc_m1aius/f1.bed -b /tmp/tmpc_m1aius/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpx07zdcg6/f1.bed -b /tmp/tmpx07zdcg6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnh4ujpt7/f1.bed -b /tmp/tmpnh4ujpt7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6tp3kyyi/f1.bed -b /tmp/tmp6tp3kyyi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpy9_qf66e/f1.bed -b /tmp/tmpy9_qf66e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpo9kpudux/f1.bed -b /tmp/tmpo9kpudux/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp166o5d9o/f1.bed -b /tmp/tmp166o5d9o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpuz4xvs88/f1.bed -b /tmp/tmpuz4xvs88/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpupxrv751/f1.bed -b /tmp/tmpupxrv751/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgsn1ci7t/f1.bed -b /tmp/tmpgsn1ci7t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7dqabf76/f1.bed -b /tmp/tmp7dqabf76/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjt05c7e5/f1.bed -b /tmp/tmpjt05c7e5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6v19yd7d/f1.bed -b /tmp/tmp6v19yd7d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9xhlnuqm/f1.bed -b /tmp/tmp9xhlnuqm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6kxo432m/f1.bed -b /tmp/tmp6kxo432m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1w4bfxk2/f1.bed -b /tmp/tmp1w4bfxk2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpf9j4el7f/f1.bed -b /tmp/tmpf9j4el7f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp51giqdzg/f1.bed -b /tmp/tmp51giqdzg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpt97ofdz9/f1.bed -b /tmp/tmpt97ofdz9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmps5e2hwgl/f1.bed -b /tmp/tmps5e2hwgl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpj096u5l_/f1.bed -b /tmp/tmpj096u5l_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpupa2zhw1/f1.bed -b /tmp/tmpupa2zhw1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3kn_j34l/f1.bed -b /tmp/tmp3kn_j34l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2n8bxh0f/f1.bed -b /tmp/tmp2n8bxh0f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbz3fl80w/f1.bed -b /tmp/tmpbz3fl80w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpw7hnh916/f1.bed -b /tmp/tmpw7hnh916/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpfg930vuh/f1.bed -b /tmp/tmpfg930vuh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpe4m7bnli/f1.bed -b /tmp/tmpe4m7bnli/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpk2nr47z8/f1.bed -b /tmp/tmpk2nr47z8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqu6h4xvj/f1.bed -b /tmp/tmpqu6h4xvj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1zw72wpv/f1.bed -b /tmp/tmp1zw72wpv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpk7cbx6y5/f1.bed -b /tmp/tmpk7cbx6y5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmperh593qr/f1.bed -b /tmp/tmperh593qr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpywg6y7yg/f1.bed -b /tmp/tmpywg6y7yg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp682dlsoj/f1.bed -b /tmp/tmp682dlsoj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjabdm_79/f1.bed -b /tmp/tmpjabdm_79/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1z4fyrf4/f1.bed -b /tmp/tmp1z4fyrf4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqc8wugi9/f1.bed -b /tmp/tmpqc8wugi9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmps6wh0u6b/f1.bed -b /tmp/tmps6wh0u6b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp00uexjjr/f1.bed -b /tmp/tmp00uexjjr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpc10w7yg8/f1.bed -b /tmp/tmpc10w7yg8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmps7mco0jl/f1.bed -b /tmp/tmps7mco0jl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpufi31em4/f1.bed -b /tmp/tmpufi31em4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp4qm8w1nl/f1.bed -b /tmp/tmp4qm8w1nl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpyguv79p5/f1.bed -b /tmp/tmpyguv79p5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp59objto2/f1.bed -b /tmp/tmp59objto2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9zjqvzt7/f1.bed -b /tmp/tmp9zjqvzt7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmputhhyc0w/f1.bed -b /tmp/tmputhhyc0w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmph6dl5aed/f1.bed -b /tmp/tmph6dl5aed/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2i9wifk8/f1.bed -b /tmp/tmp2i9wifk8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbdm7ra7w/f1.bed -b /tmp/tmpbdm7ra7w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpyfh6di__/f1.bed -b /tmp/tmpyfh6di__/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5qh48yyd/f1.bed -b /tmp/tmp5qh48yyd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3kurto7x/f1.bed -b /tmp/tmp3kurto7x/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmppxntavmo/f1.bed -b /tmp/tmppxntavmo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpllb05ip1/f1.bed -b /tmp/tmpllb05ip1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjdi5yks1/f1.bed -b /tmp/tmpjdi5yks1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpy0513hlm/f1.bed -b /tmp/tmpy0513hlm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpczw1576w/f1.bed -b /tmp/tmpczw1576w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpaktfp4kj/f1.bed -b /tmp/tmpaktfp4kj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgmaditvn/f1.bed -b /tmp/tmpgmaditvn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2vlg98uh/f1.bed -b /tmp/tmp2vlg98uh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpksmn68c9/f1.bed -b /tmp/tmpksmn68c9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_ldu5quc/f1.bed -b /tmp/tmp_ldu5quc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpllkz5rlk/f1.bed -b /tmp/tmpllkz5rlk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpyopguumw/f1.bed -b /tmp/tmpyopguumw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgq7n9ip8/f1.bed -b /tmp/tmpgq7n9ip8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2zo_8jf5/f1.bed -b /tmp/tmp2zo_8jf5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdh4dwsxv/f1.bed -b /tmp/tmpdh4dwsxv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7qo52hdy/f1.bed -b /tmp/tmp7qo52hdy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp68snlu2f/f1.bed -b /tmp/tmp68snlu2f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpl3at5peb/f1.bed -b /tmp/tmpl3at5peb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmu1es47o/f1.bed -b /tmp/tmpmu1es47o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp02v0eibh/f1.bed -b /tmp/tmp02v0eibh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprez9wf6h/f1.bed -b /tmp/tmprez9wf6h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpl5l7m450/f1.bed -b /tmp/tmpl5l7m450/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp813163xw/f1.bed -b /tmp/tmp813163xw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5e0hj_uv/f1.bed -b /tmp/tmp5e0hj_uv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp59i3u3pe/f1.bed -b /tmp/tmp59i3u3pe/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9t7stq4b/f1.bed -b /tmp/tmp9t7stq4b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpr5sigwic/f1.bed -b /tmp/tmpr5sigwic/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp33bjwhkk/f1.bed -b /tmp/tmp33bjwhkk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_xhbnzha/f1.bed -b /tmp/tmp_xhbnzha/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5xc77h5o/f1.bed -b /tmp/tmp5xc77h5o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmproj5mz2p/f1.bed -b /tmp/tmproj5mz2p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7m520ftz/f1.bed -b /tmp/tmp7m520ftz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpux7hjg7f/f1.bed -b /tmp/tmpux7hjg7f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_io9umfb/f1.bed -b /tmp/tmp_io9umfb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmedwqbq0/f1.bed -b /tmp/tmpmedwqbq0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpudsmqd38/f1.bed -b /tmp/tmpudsmqd38/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpk_8gi2jv/f1.bed -b /tmp/tmpk_8gi2jv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprdkovdpy/f1.bed -b /tmp/tmprdkovdpy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdqvustt3/f1.bed -b /tmp/tmpdqvustt3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpgzxncd1k/f1.bed -b /tmp/tmpgzxncd1k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpddfgpk3v/f1.bed -b /tmp/tmpddfgpk3v/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpey5eys4t/f1.bed -b /tmp/tmpey5eys4t/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmhjh1f5i/f1.bed -b /tmp/tmpmhjh1f5i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmp4jicni/f1.bed -b /tmp/tmpmp4jicni/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpw3_ug89c/f1.bed -b /tmp/tmpw3_ug89c/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpek_w_mmd/f1.bed -b /tmp/tmpek_w_mmd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpkr_x0zaz/f1.bed -b /tmp/tmpkr_x0zaz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1a9n8xq6/f1.bed -b /tmp/tmp1a9n8xq6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpx1jcacff/f1.bed -b /tmp/tmpx1jcacff/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjhl3gzht/f1.bed -b /tmp/tmpjhl3gzht/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpodmvumvt/f1.bed -b /tmp/tmpodmvumvt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_ypvrbjx/f1.bed -b /tmp/tmp_ypvrbjx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpm7szpp8p/f1.bed -b /tmp/tmpm7szpp8p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpr2lmhkac/f1.bed -b /tmp/tmpr2lmhkac/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpsqtdtvnt/f1.bed -b /tmp/tmpsqtdtvnt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpyl6xl5fx/f1.bed -b /tmp/tmpyl6xl5fx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpzle_ao85/f1.bed -b /tmp/tmpzle_ao85/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpg2lw9khc/f1.bed -b /tmp/tmpg2lw9khc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnhnvvqee/f1.bed -b /tmp/tmpnhnvvqee/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpclxd5ixj/f1.bed -b /tmp/tmpclxd5ixj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmph38l98bo/f1.bed -b /tmp/tmph38l98bo/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpx0icpg0p/f1.bed -b /tmp/tmpx0icpg0p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpr0hju1wv/f1.bed -b /tmp/tmpr0hju1wv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_yrlbp9f/f1.bed -b /tmp/tmp_yrlbp9f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp8a7k5lvi/f1.bed -b /tmp/tmp8a7k5lvi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2qi6yeln/f1.bed -b /tmp/tmp2qi6yeln/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpepbzd473/f1.bed -b /tmp/tmpepbzd473/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbphp_wq0/f1.bed -b /tmp/tmpbphp_wq0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6akilt1b/f1.bed -b /tmp/tmp6akilt1b/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1hth1p6l/f1.bed -b /tmp/tmp1hth1p6l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp4yiooo4j/f1.bed -b /tmp/tmp4yiooo4j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp405dvqfc/f1.bed -b /tmp/tmp405dvqfc/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmphxw8lp94/f1.bed -b /tmp/tmphxw8lp94/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpyp0dmks1/f1.bed -b /tmp/tmpyp0dmks1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp0djat3l0/f1.bed -b /tmp/tmp0djat3l0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpvg8mfqzi/f1.bed -b /tmp/tmpvg8mfqzi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwty03_x3/f1.bed -b /tmp/tmpwty03_x3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpv6ykfbwu/f1.bed -b /tmp/tmpv6ykfbwu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpzc7vatsi/f1.bed -b /tmp/tmpzc7vatsi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7zl3i740/f1.bed -b /tmp/tmp7zl3i740/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp8e7vg65y/f1.bed -b /tmp/tmp8e7vg65y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6apilj0k/f1.bed -b /tmp/tmp6apilj0k/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5vpipl_f/f1.bed -b /tmp/tmp5vpipl_f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6cc_hifd/f1.bed -b /tmp/tmp6cc_hifd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpf7laz5ja/f1.bed -b /tmp/tmpf7laz5ja/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9yw3r6k_/f1.bed -b /tmp/tmp9yw3r6k_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmptgg9277f/f1.bed -b /tmp/tmptgg9277f/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpvcisw49_/f1.bed -b /tmp/tmpvcisw49_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpd5sft0fs/f1.bed -b /tmp/tmpd5sft0fs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9b5yurrx/f1.bed -b /tmp/tmp9b5yurrx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3m7_38d3/f1.bed -b /tmp/tmp3m7_38d3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp23d1bvs4/f1.bed -b /tmp/tmp23d1bvs4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp9wuz2__o/f1.bed -b /tmp/tmp9wuz2__o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpuwnhay3a/f1.bed -b /tmp/tmpuwnhay3a/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpefd1rbw3/f1.bed -b /tmp/tmpefd1rbw3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpuapx4bq2/f1.bed -b /tmp/tmpuapx4bq2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpw6aucj0r/f1.bed -b /tmp/tmpw6aucj0r/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpl41_l2et/f1.bed -b /tmp/tmpl41_l2et/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpuj7erjj8/f1.bed -b /tmp/tmpuj7erjj8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdm_6npyt/f1.bed -b /tmp/tmpdm_6npyt/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbzuavcn6/f1.bed -b /tmp/tmpbzuavcn6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpx_lfz_w3/f1.bed -b /tmp/tmpx_lfz_w3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpajdhoair/f1.bed -b /tmp/tmpajdhoair/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmikv0r7j/f1.bed -b /tmp/tmpmikv0r7j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpxzjsgljl/f1.bed -b /tmp/tmpxzjsgljl/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdc62d77l/f1.bed -b /tmp/tmpdc62d77l/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpv7lqbo20/f1.bed -b /tmp/tmpv7lqbo20/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqh4zkynq/f1.bed -b /tmp/tmpqh4zkynq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmplac3ab3q/f1.bed -b /tmp/tmplac3ab3q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwisucjqi/f1.bed -b /tmp/tmpwisucjqi/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp3h7sqhkm/f1.bed -b /tmp/tmp3h7sqhkm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqs0ffivm/f1.bed -b /tmp/tmpqs0ffivm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpna20xlvd/f1.bed -b /tmp/tmpna20xlvd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwfywawym/f1.bed -b /tmp/tmpwfywawym/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp8wx6uivu/f1.bed -b /tmp/tmp8wx6uivu/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp13eybgog/f1.bed -b /tmp/tmp13eybgog/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmppx_wk1r7/f1.bed -b /tmp/tmppx_wk1r7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmprs368w5i/f1.bed -b /tmp/tmprs368w5i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6wxeyaxx/f1.bed -b /tmp/tmp6wxeyaxx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmph141dcy3/f1.bed -b /tmp/tmph141dcy3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpsrv0xsrp/f1.bed -b /tmp/tmpsrv0xsrp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp955ltw8e/f1.bed -b /tmp/tmp955ltw8e/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp_krw8i8i/f1.bed -b /tmp/tmp_krw8i8i/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpw614qun8/f1.bed -b /tmp/tmpw614qun8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpy77dgjhk/f1.bed -b /tmp/tmpy77dgjhk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpicpvvkfs/f1.bed -b /tmp/tmpicpvvkfs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbb_gh6vq/f1.bed -b /tmp/tmpbb_gh6vq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1um9z9tm/f1.bed -b /tmp/tmp1um9z9tm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2b5hk4fk/f1.bed -b /tmp/tmp2b5hk4fk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp5q1ccb4j/f1.bed -b /tmp/tmp5q1ccb4j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2l183qmv/f1.bed -b /tmp/tmp2l183qmv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmlw58z0p/f1.bed -b /tmp/tmpmlw58z0p/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpzienk2lh/f1.bed -b /tmp/tmpzienk2lh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpl8k2xvy3/f1.bed -b /tmp/tmpl8k2xvy3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpx9jc0diw/f1.bed -b /tmp/tmpx9jc0diw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmppe6au14w/f1.bed -b /tmp/tmppe6au14w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpqmjuat_8/f1.bed -b /tmp/tmpqmjuat_8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp1j06y4c9/f1.bed -b /tmp/tmp1j06y4c9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpz66rxwx3/f1.bed -b /tmp/tmpz66rxwx3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7pqplvju/f1.bed -b /tmp/tmp7pqplvju/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp4wtvkdoy/f1.bed -b /tmp/tmp4wtvkdoy/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpazn5j6sj/f1.bed -b /tmp/tmpazn5j6sj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpwg9dcs54/f1.bed -b /tmp/tmpwg9dcs54/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpnwb1ah24/f1.bed -b /tmp/tmpnwb1ah24/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbbiz0gpk/f1.bed -b /tmp/tmpbbiz0gpk/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmppu5kcx_4/f1.bed -b /tmp/tmppu5kcx_4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpg9_mgsqg/f1.bed -b /tmp/tmpg9_mgsqg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp66rwdeis/f1.bed -b /tmp/tmp66rwdeis/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpjexe3lx_/f1.bed -b /tmp/tmpjexe3lx_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp66f8x4zb/f1.bed -b /tmp/tmp66f8x4zb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpmd684kwj/f1.bed -b /tmp/tmpmd684kwj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp7m7xm6eh/f1.bed -b /tmp/tmp7m7xm6eh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpo7tnsg5g/f1.bed -b /tmp/tmpo7tnsg5g/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting __________ test_three_in_a_row[strandedness_chain109-method_chain109] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ___________ test_three_in_a_row[strandedness_chain98-method_chain98] ___________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 248 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') __________________ test_k_nearest[downstream-False-same-last] __________________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1s.values, d2e.values, d1s.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=False, | strandedness='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 39 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGDFEADi2Axc=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1e.values, d2s.values, d1e.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=False, | strandedness='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppqfee5vj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppqfee5vj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnslnl37u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnslnl37u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb7y3k46q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb7y3k46q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy41jtfr8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy41jtfr8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5k127tt6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5k127tt6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp63b8v0js/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp63b8v0js/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpamuh31yn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpamuh31yn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3zb33bof/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3zb33bof/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5u359bkm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5u359bkm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaamp_g8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaamp_g8_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaq_x79tt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaq_x79tt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuojrqlli/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuojrqlli/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk_bxpv8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_bxpv8_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkj29ybxw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkj29ybxw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi2q51hoe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi2q51hoe/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpas_emfs6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpas_emfs6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf1_93v3i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf1_93v3i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf85jnfuq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf85jnfuq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8qhel3xq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8qhel3xq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprw501qn_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprw501qn_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpru0t1war/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpru0t1war/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxfhs4lkw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxfhs4lkw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptiup6a6o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptiup6a6o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp66npewob/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp66npewob/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0nc7li2p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0nc7li2p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwmayb4rd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwmayb4rd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd4ud8uls/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd4ud8uls/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9qn6ymto/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qn6ymto/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgxhg6tem/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgxhg6tem/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyyb1z0jn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyyb1z0jn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppn7_srrd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppn7_srrd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg261lzdd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg261lzdd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6wshhmhy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6wshhmhy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5e8t74kd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5e8t74kd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe4hiqu2q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe4hiqu2q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyzpbtps3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyzpbtps3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv_w2qzwt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv_w2qzwt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk0krzceo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk0krzceo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpylyccm1c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpylyccm1c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxdpz9b_s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxdpz9b_s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp36yn9rut/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36yn9rut/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq0j7xlsr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq0j7xlsr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx8fmud8y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx8fmud8y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqlf7qktx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqlf7qktx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplmipepfm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplmipepfm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc0qb5ulc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc0qb5ulc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcwsczpaj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcwsczpaj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1bd1li6n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1bd1li6n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6st3adrn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6st3adrn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgsw36e7s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgsw36e7s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7qkkzw9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qkkzw9w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn7kd0sju/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn7kd0sju/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp86p6mtf8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp86p6mtf8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpshe7yytp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpshe7yytp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp91srso2b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp91srso2b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6qd5b0ur/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6qd5b0ur/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp98_5d0ry/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp98_5d0ry/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnebshtvh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnebshtvh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4j115cux/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4j115cux/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzritngjb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzritngjb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptadszfx8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptadszfx8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe7zf66se/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7zf66se/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7qongo90/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qongo90/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpskxpllm8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpskxpllm8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe2e_wf6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe2e_wf6y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl50tom28/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl50tom28/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpodpa8hj6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpodpa8hj6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx6k1q90z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx6k1q90z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9a8f3083/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9a8f3083/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpetdujest/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpetdujest/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp791inf89/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp791inf89/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6avmk3t0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6avmk3t0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv72iab99/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv72iab99/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprw1d9zor/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprw1d9zor/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyhafj9ip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyhafj9ip/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpee0py6ff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpee0py6ff/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpww1nrtw_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpww1nrtw_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpunhyzehw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpunhyzehw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz99hkk4h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz99hkk4h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpji5_b6i2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpji5_b6i2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplgvdbff5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplgvdbff5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmjtq0gz8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmjtq0gz8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpouhmfq8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpouhmfq8_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpev0fscyw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpev0fscyw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpskeizvck/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpskeizvck/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph3fipd44/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph3fipd44/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb83s53_p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb83s53_p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdejmg6h8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdejmg6h8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ee8ulxw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ee8ulxw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps89ynqbo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps89ynqbo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7rf5rc9u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7rf5rc9u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiz0k_9o2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiz0k_9o2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwlu8er7c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwlu8er7c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptar_kepu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptar_kepu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprovq_kbc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprovq_kbc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmru_ezi4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmru_ezi4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkbc9tw04/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkbc9tw04/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxywd73u7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxywd73u7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxgqriddv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxgqriddv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa9dzerfe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa9dzerfe/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph95t0q5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph95t0q5d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfuoxet7m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfuoxet7m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn7u6wxay/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn7u6wxay/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpds9lb_6g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpds9lb_6g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm371g87u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm371g87u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpim9_6_73/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpim9_6_73/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3zmjxpgj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3zmjxpgj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw395zttg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw395zttg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxangiusn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxangiusn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0pqmyhi2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0pqmyhi2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplle86sig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplle86sig/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqeryobur/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqeryobur/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp02trct1r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp02trct1r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt3dmflw1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt3dmflw1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt23rompg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt23rompg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnbr6l8kk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnbr6l8kk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn_t0enmz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn_t0enmz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4e1mkqn0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4e1mkqn0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeu6sxr7r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeu6sxr7r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgj3kthxz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgj3kthxz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2uiclq4a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2uiclq4a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8blelznk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8blelznk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkxessjk_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkxessjk_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj5ft6nt5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5ft6nt5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpteggon6j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpteggon6j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6gb28lf7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6gb28lf7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqhqb06ta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqhqb06ta/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg1nouuxf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg1nouuxf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdz38ilap/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdz38ilap/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6gmfa15r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6gmfa15r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcuu0luhg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcuu0luhg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy5g_u7s4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy5g_u7s4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk_uv1crb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_uv1crb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_tu7qlb9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_tu7qlb9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr69wnix8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr69wnix8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxta7adv_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxta7adv_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsnwdnuky/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsnwdnuky/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu93he0v9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu93he0v9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6k_c11_k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6k_c11_k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgml5szkc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgml5szkc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjz0hgim9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjz0hgim9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp75aius0i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp75aius0i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9hchtcfw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9hchtcfw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8vya_iud/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8vya_iud/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain17-method_chain17] ___________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 5843755 | 5843756 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 5843755 | 5843756 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3R2f2bO6MLQOuMso7Nj7X0gc7pCNaMjI6Oze38aA4MjEDI6sjpHamszAtmMcMToHCy5HKIRpooBpAqhAEiCJeAiAALkE4U=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9999999 | 10001729 | a | 0 | ... | | chr2 | 6817555 | 6819285 | a | 0 | ... | | chr2 | 631704 | 633434 | a | 0 | ... | | chr2 | 1026316 | 1028046 | a | 0 | ... | | chr2 | 575042 | 576772 | a | 0 | ... | | chr2 | 6528580 | 6530310 | a | 0 | ... | | chr2 | 3296174 | 3297904 | a | 0 | ... | | chr2 | 5934357 | 5936087 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain66-method_chain66] ___________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGRyYGINuRgREhwggWhIowwhADAHTLBGE=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6313712 | 6320259 | a | 0 | ... | | chr1 | 1850672 | 1856222 | a | 0 | ... | | chr1 | 2824074 | 2825648 | a | 0 | ... | | chr1 | 8641467 | 8647017 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr10 | 8108861 | 8117245 | a | 0 | ... | | chr17 | 4820923 | 4824876 | a | 0 | ... | | chr19 | 2874 | 11528 | a | 0 | ... | | chrY | 935630 | 944701 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6313712 | 6320259 | a | 0 | ... | | chr1 | 1850672 | 1856222 | a | 0 | ... | | chr1 | 2824074 | 2825648 | a | 0 | ... | | chr1 | 8641467 | 8647017 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr10 | 8108861 | 8117245 | a | 0 | ... | | chr17 | 4820923 | 4824876 | a | 0 | ... | | chr19 | 2874 | 11528 | a | 0 | ... | | chrY | 935630 | 944701 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8466897 | 8469575 | a | 0 | ... | | chr1 | 8891475 | 8900011 | a | 0 | ... | | chr1 | 8986010 | 8993103 | a | 0 | ... | | chr1 | 496536 | 504446 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr7 | 4237479 | 4239641 | a | 0 | ... | | chr7 | 7381595 | 7386893 | a | 0 | ... | | chr8 | 2376252 | 2377939 | a | 0 | ... | | chr15 | 1909697 | 1919125 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain71-method_chain71] ___________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 183 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZHRkZGBwBEJGIMEEZDKC2VBBMJcRwgBDBgBzHwSi') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 | /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 | (and 83 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') 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('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________________ test_nearest[downstream-True-opposite] ____________________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.End) | ^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 129 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwZGR0ZHBkAjHAbEYoC4wYADLsAtk=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.Start, ocdf.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_ends.values - 1, right_starts.values, right_indexes) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 126 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGAAYihiYATzgZDBkQkiCAAwXwLX') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | ~~~~~~~~~~~~~~~~~~~^ | lcol, | ^^^^^ | ...<12 lines>... | check_flags=False, | ^^^^^^^^^^^^^^^^^^ | ) | ^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 464 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGAAYihiYETlMwIAKfkClg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbu_q7yik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbu_q7yik/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj359xbmp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj359xbmp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdmp_j5mf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdmp_j5mf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjp6najmr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjp6najmr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnh9lmy2_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnh9lmy2_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxaa5m6wy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxaa5m6wy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_jgxpoiw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_jgxpoiw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp34wxnq3r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp34wxnq3r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpih5u6jdm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpih5u6jdm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi2_x3upk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi2_x3upk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2hslgvmw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2hslgvmw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0mup_h89/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0mup_h89/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkc72gfy9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkc72gfy9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2pdk1kyz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2pdk1kyz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6cc8bqt1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6cc8bqt1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpugq_rib1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpugq_rib1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp073qwjjf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp073qwjjf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcneaoz3_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcneaoz3_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8f4vxarl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8f4vxarl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplz4n_lcb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplz4n_lcb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn_591bvd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn_591bvd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg0m4dtd2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg0m4dtd2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph1xuy2s4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph1xuy2s4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ihcq5ki/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ihcq5ki/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgongxys_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgongxys_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpie19i8za/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpie19i8za/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi_oytyr1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi_oytyr1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr6feusic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr6feusic/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3g00ekjp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3g00ekjp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz1rw0mxm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz1rw0mxm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6ijod3dp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ijod3dp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo36_35jd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo36_35jd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx_vpdh4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx_vpdh4v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpze9cnybw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpze9cnybw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3g0wuinj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3g0wuinj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiupd0oyg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiupd0oyg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwygrd77k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwygrd77k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp382s0xqm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp382s0xqm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp58nyjx2l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp58nyjx2l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp17x9e1c8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp17x9e1c8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph6hcowi9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph6hcowi9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiksm81by/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiksm81by/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoihrbqjn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoihrbqjn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfqemh_0c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfqemh_0c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp85e7ygz7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp85e7ygz7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzpu2428p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzpu2428p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa5bc_9ef/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa5bc_9ef/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyof5wtsm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyof5wtsm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8wwqyypl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8wwqyypl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7fuoi675/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7fuoi675/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzsozbfl4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzsozbfl4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_lg7wdis/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_lg7wdis/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe8agdqs3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8agdqs3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpayeoys_q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpayeoys_q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjb3dxdf2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjb3dxdf2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0g6otvbu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0g6otvbu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprln0h5o_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprln0h5o_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzh8jr8z2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzh8jr8z2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj50ke0y6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj50ke0y6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp00g__bg1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00g__bg1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpghb0zzfa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpghb0zzfa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6aix2d5l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6aix2d5l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk9yo9xw3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk9yo9xw3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_v9mn9fs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_v9mn9fs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmposmefeec/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmposmefeec/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0h9kjh8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0h9kjh8_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplf2v9or2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplf2v9or2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3l1lhcze/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3l1lhcze/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv7e0jn8d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv7e0jn8d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpetkbya9s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpetkbya9s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq37pcobh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq37pcobh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp59mwhdry/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp59mwhdry/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp41e86yeb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp41e86yeb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjhpo430o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjhpo430o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgf9h9qap/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgf9h9qap/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0ohrz7hi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ohrz7hi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 + 0 9 chr1 1 2 - 0 10 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 + 0 9 chr1 1 2 - 0 10 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 + 0 9 chr1 1 2 - 0 10 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 + 0 9 chr1 1 2 - 0 10 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 + 0 9 chr1 1 2 - 0 10 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxyi2h390/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxyi2h390/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 - 0 9 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 - 0 9 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 - 0 9 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 - 0 9 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 - 0 9 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo9shz5os/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo9shz5os/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm0wg2nla/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm0wg2nla/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_d2gqe1y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_d2gqe1y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 - 0 9 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 - 0 9 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 - 0 9 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 - 0 9 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 - 0 9 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplnn7k31j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplnn7k31j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0tbdj325/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0tbdj325/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1iq1l_vs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1iq1l_vs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9s9vx7cc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9s9vx7cc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpph5n7kpe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpph5n7kpe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph6ov2taq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph6ov2taq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm4f_uyd7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm4f_uyd7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_mhs4wzh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_mhs4wzh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcdeuvv_7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcdeuvv_7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplxv9bz51/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplxv9bz51/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp72pkjsnv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp72pkjsnv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwv_5dcob/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwv_5dcob/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4e0zdvfd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4e0zdvfd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzvb5fop3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzvb5fop3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8b_i91jf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8b_i91jf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8s67m1g1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8s67m1g1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptbd0n9f5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptbd0n9f5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcs78d3ip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcs78d3ip/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw34rvvar/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw34rvvar/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4cr4mg4t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4cr4mg4t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplqfyib0t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplqfyib0t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8bbmbz87/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8bbmbz87/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp6tx_600/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp6tx_600/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp57s8wabv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp57s8wabv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb9zm2025/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb9zm2025/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpue1dfdvz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpue1dfdvz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpykrrowwk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpykrrowwk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6_cltl4_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6_cltl4_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4f09wyz2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4f09wyz2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpusby612b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpusby612b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphdk2h_e7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphdk2h_e7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5vbaogv2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5vbaogv2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb1f79f24/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb1f79f24/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq1isidwv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq1isidwv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyiqe18jy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyiqe18jy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgwlrky3t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgwlrky3t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbgym03vr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbgym03vr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp39_b_ci3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp39_b_ci3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfu4odk_z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfu4odk_z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj7w1di11/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj7w1di11/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9sc93g7a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9sc93g7a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq6cycudm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq6cycudm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl4sfanvk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl4sfanvk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqm8dgo4d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqm8dgo4d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmfy8ygkp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmfy8ygkp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp913kvizm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp913kvizm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp860ly_9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp860ly_9w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnz3p3kp7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnz3p3kp7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqra6hcfr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqra6hcfr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvx9k14if/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvx9k14if/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5maioios/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5maioios/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw1kmb5km/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw1kmb5km/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp78p0xd5u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp78p0xd5u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbitvvjo7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbitvvjo7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfymm_tzz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfymm_tzz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1x7ipc5w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1x7ipc5w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu6io5t9l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu6io5t9l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3almh7ts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3almh7ts/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp24y_faeh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp24y_faeh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsb0esfig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsb0esfig/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzc95vx4s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzc95vx4s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq03y7k45/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq03y7k45/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp86dkw_49/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp86dkw_49/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl42b2tl7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl42b2tl7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsc8qrxoe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsc8qrxoe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2u3u93nx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2u3u93nx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmperf00y3e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmperf00y3e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_weksbgz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_weksbgz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi_nqqrzs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi_nqqrzs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0clyf8ya/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0clyf8ya/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1mop15y6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1mop15y6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6gtfz9v0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6gtfz9v0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwjtfuaqt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwjtfuaqt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppix5vpot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppix5vpot/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsi84bq4h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsi84bq4h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp02rq4xqc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp02rq4xqc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7gk6vs3i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7gk6vs3i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpibgot5yk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpibgot5yk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_dd84dm7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_dd84dm7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4llc5lz8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4llc5lz8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpshz1qs7h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpshz1qs7h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwu_7crbz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwu_7crbz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb06sk23b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb06sk23b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqktgyeuc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqktgyeuc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyyz1eby1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyyz1eby1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt0cap4s1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt0cap4s1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmfy3t7xq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmfy3t7xq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjmt4wd9j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjmt4wd9j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7sy6j2a9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7sy6j2a9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpukp7h9qi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpukp7h9qi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo0dikx7s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo0dikx7s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp86nfgf55/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp86nfgf55/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_j3ibv78/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_j3ibv78/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1cj951lw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1cj951lw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 1 7470 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7470 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 7470 - 0 df2 Chromosome Start End Strand Distance 1 chr1 1 7470 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 7470 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 7470 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp41md11ft/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp41md11ft/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 1 7470 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7470 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 7470 - 0 df2 Chromosome Start End Strand Distance 1 chr1 1 7470 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 7470 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 7470 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3gont_6j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3gont_6j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdbgref07/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdbgref07/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 1 7470 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7470 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 7470 - 0 df2 Chromosome Start End Strand Distance 1 chr1 1 7470 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 7470 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 7470 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe97ca0i8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe97ca0i8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1n8uy759/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1n8uy759/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplfhmrk5w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplfhmrk5w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptgpyq1ca/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptgpyq1ca/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3z8jdadi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3z8jdadi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpftzaq0w0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpftzaq0w0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpthusl3mp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpthusl3mp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpegy_ubdf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpegy_ubdf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbkvfxfx2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbkvfxfx2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxsmm4ypc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxsmm4ypc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz6sz8lbp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz6sz8lbp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbdx7tnbd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbdx7tnbd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpll750aho/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpll750aho/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 - 0 9 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 - 0 9 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 - 0 9 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 - 0 9 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 6 chr1 1 2 + 0 7 chr1 1 2 + 0 8 chr1 1 2 - 0 9 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk_9yrl6q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_9yrl6q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi4jdk42b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi4jdk42b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyqs0zj27/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqs0zj27/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpldvp5ksh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpldvp5ksh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx1cwhkzo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx1cwhkzo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxsbx7nvc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxsbx7nvc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8az4j6ga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8az4j6ga/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqn03fsmh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqn03fsmh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl_0lh96_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl_0lh96_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxrq8eyuf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxrq8eyuf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwosbydax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwosbydax/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvcb80fk8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvcb80fk8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpauygy92w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpauygy92w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp80y_yqj8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp80y_yqj8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_kpatx0h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_kpatx0h/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpht1ukj2c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpht1ukj2c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcifpdjz2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcifpdjz2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7k3btrv9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7k3btrv9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3dfqpla6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3dfqpla6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1zoo0ihi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1zoo0ihi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplgq7hchc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplgq7hchc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp14t_m4ee/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp14t_m4ee/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx_dtk0ry/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx_dtk0ry/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpec_zrvih/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpec_zrvih/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpauwrk8f5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpauwrk8f5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbi8w0xve/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbi8w0xve/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplic47da6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplic47da6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_76q3daq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_76q3daq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi7hd1mqh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi7hd1mqh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdq65_02m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdq65_02m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjrftv4tx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjrftv4tx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6j20zusw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6j20zusw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj0cwc6z1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj0cwc6z1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi2f3wljn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi2f3wljn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl0ah4ih3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0ah4ih3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsd5vuwyy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsd5vuwyy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpza5ao50b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpza5ao50b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4g73deti/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4g73deti/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsnbjaf5_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsnbjaf5_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf4tc46on/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf4tc46on/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe6uxn4rw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe6uxn4rw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq0x11kgk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq0x11kgk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqwe486me/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqwe486me/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5_01t9t4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5_01t9t4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwum7bvws/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwum7bvws/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx281vhv5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx281vhv5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe1j42fhp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe1j42fhp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpccmh69_0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpccmh69_0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpitioac8m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpitioac8m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxfmn50z3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxfmn50z3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8pyob20s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8pyob20s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7z8apryy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7z8apryy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxscy_q60/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxscy_q60/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp99gwln4p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp99gwln4p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjg0q8ir7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjg0q8ir7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe9dblbh6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe9dblbh6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoc5qi_2x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoc5qi_2x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxnbbe99e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxnbbe99e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx4tbe7ju/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx4tbe7ju/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnas22jft/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnas22jft/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2h6ng65y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2h6ng65y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdrqbi5oj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdrqbi5oj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmezjp0pu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmezjp0pu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfjfpiulr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfjfpiulr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoi50mka1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoi50mka1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw7gmevk8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw7gmevk8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo1yck88x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo1yck88x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvu1erlkc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvu1erlkc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1rvk6_37/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1rvk6_37/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ___________ test_three_in_a_row[strandedness_chain26-method_chain26] ___________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 | (and 27 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGGEijECCCSEOhgwAZhcEYQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', False), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 | (and 24 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _________________ test_k_nearest[downstream-False-False-last] __________________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1s.values, d2e.values, d1s.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=False, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:19 | (and 37 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGMEijDDEAAAx1ALW') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1e.values, d2s.values, d1e.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=False, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:42 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:46 | (and 37 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp11r23ppx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp11r23ppx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprt1ltqt2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprt1ltqt2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpto19o9f5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpto19o9f5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmajnd4c_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmajnd4c_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_ht21lwd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ht21lwd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7736b2z8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7736b2z8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgw0lbb6c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgw0lbb6c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6rtajsdo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6rtajsdo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcj_taojn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcj_taojn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp_i2w5ja/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_i2w5ja/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp498w7yq0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp498w7yq0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm8azdqbj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm8azdqbj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpklz64634/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpklz64634/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuuknhm4w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuuknhm4w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbrlmnth8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbrlmnth8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpahmfdpr0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpahmfdpr0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe23op3m7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe23op3m7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg9avq3fz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg9avq3fz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu9s6im2k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu9s6im2k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe12fqac_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe12fqac_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1f93byuf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1f93byuf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7nd_3kai/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7nd_3kai/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7a9x0z2f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7a9x0z2f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcgnzny1x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcgnzny1x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqpmrud_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqpmrud_h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcpk8lt3x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcpk8lt3x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppsm8d_w4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppsm8d_w4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxqn5i4ry/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxqn5i4ry/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfxbdvo51/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfxbdvo51/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpln_zktm6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpln_zktm6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0104x4cb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0104x4cb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_koek45k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_koek45k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1due8ika/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1due8ika/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp87pwjnj3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp87pwjnj3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6ihkrufr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ihkrufr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppgacrvc7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppgacrvc7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt4u5e1ou/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt4u5e1ou/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp94f_3gv_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp94f_3gv_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiv56bdm8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiv56bdm8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz8mgw0_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz8mgw0_e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpai991id_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpai991id_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptus7bqpp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptus7bqpp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq1n2lyrd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq1n2lyrd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbn1wd4v0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbn1wd4v0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbkt5m84h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbkt5m84h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6x6a89mw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6x6a89mw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3a94sp76/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3a94sp76/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptazc4vqc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptazc4vqc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpluzxuyv5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpluzxuyv5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuxm6d22k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuxm6d22k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp8n1gi50/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp8n1gi50/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplgr2fd_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplgr2fd_x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvibzrzis/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvibzrzis/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj7nfh1ez/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj7nfh1ez/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2bhj1m4u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2bhj1m4u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2n0a44e0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2n0a44e0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8lz8u2s6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8lz8u2s6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps86r_c97/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps86r_c97/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp30w0tlzz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp30w0tlzz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnxq971x8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnxq971x8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn9pnr41p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn9pnr41p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq4ol5fmo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq4ol5fmo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpixyr4p_m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpixyr4p_m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb0_3kcwn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb0_3kcwn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkldww8q5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkldww8q5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3lkpenfm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3lkpenfm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0_5amyzh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_5amyzh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpswv5zuwz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpswv5zuwz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwvs4aeia/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwvs4aeia/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5lylwz4m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5lylwz4m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwz447kvd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwz447kvd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptto6xzn1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptto6xzn1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdnau12cm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdnau12cm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5ph11u3u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ph11u3u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7wrh36ip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7wrh36ip/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp50r3l5jt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp50r3l5jt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbsvdtvow/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbsvdtvow/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzteoixq5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzteoixq5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdbans6zc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdbans6zc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpui5u5p6k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpui5u5p6k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpipmy37dr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpipmy37dr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9p2w0rro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9p2w0rro/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8hj99edm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8hj99edm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpum3r6xpy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpum3r6xpy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzxyvdza0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzxyvdza0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphp0w2a3t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphp0w2a3t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi2y8_sg_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi2y8_sg_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7a7v2jek/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7a7v2jek/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0cksdico/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0cksdico/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzz_mtc_g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzz_mtc_g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa3_lupgp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa3_lupgp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0m168hhf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0m168hhf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr9wi_uuv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr9wi_uuv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptpgbzbz0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptpgbzbz0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5k0exm87/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5k0exm87/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpccrjnv9y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpccrjnv9y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpehdxrowa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpehdxrowa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpox_57ayc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpox_57ayc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp46rechh3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp46rechh3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpadshfqwx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpadshfqwx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoe497_pk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoe497_pk/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. __________ test_three_in_a_row[strandedness_chain110-method_chain110] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 100 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ___________ test_three_in_a_row[strandedness_chain99-method_chain99] ___________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 116 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ________________________ test_nearest[None-True-False] _________________________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | (and 62 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGRyYGINuRgREswghDDAAx2gLW') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | ~~~~~~~~~~~~~~~~~~~^ | lcol, | ^^^^^ | ...<12 lines>... | check_flags=False, | ^^^^^^^^^^^^^^^^^^ | ) | ^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/init.py:174 | (and 459 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp38ylbcaf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp38ylbcaf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa12gnv7c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa12gnv7c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1q4lo1ac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1q4lo1ac/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphbn2vffm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphbn2vffm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 3042421 3042422 + 0 2 chr1 7673759 7673760 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7673759 | 7673760 | a | 0 | ... | | chr1 | 3042421 | 3042422 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 + 0 1 chr1 3042421 3042422 + 0 0 chr1 7673759 7673760 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 3042421 3042422 + 0 2 chr1 7673759 7673760 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 3042421 3042422 + 0 2 chr1 7673759 7673760 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 3042421 3042422 + 0 2 chr1 7673759 7673760 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp96qag1cd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp96qag1cd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqj8yompj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqj8yompj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjd9uqnse/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjd9uqnse/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt81s3z4j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt81s3z4j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp4kfmrti/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp4kfmrti/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm1_vsqvz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm1_vsqvz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5703039 5707171 + 0 1 chr1 6149086 6155077 + 0 2 chr1 6467515 6475153 + 0 3 chr10 3640896 3649670 + 0 4 chr12 8400648 8405126 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5703039 | 5707171 | a | 0 | ... | | chr1 | 6467515 | 6475153 | a | 0 | ... | | chr1 | 6149086 | 6155077 | a | 0 | ... | | chr10 | 3640896 | 3649670 | a | 0 | ... | | chr12 | 8400648 | 8405126 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr10 3640896 3649670 + 0 0 chr1 5703039 5707171 + 0 2 chr1 6149086 6155077 + 0 1 chr1 6467515 6475153 + 0 4 chr12 8400648 8405126 - 0 df2 Chromosome Start End Strand Distance 3 chr10 3640896 3649670 + 0 0 chr1 5703039 5707171 + 0 1 chr1 6149086 6155077 + 0 2 chr1 6467515 6475153 + 0 4 chr12 8400648 8405126 - 0 Actual Chromosome Start End Strand Distance 0 chr1 5703039 5707171 + 0 1 chr1 6149086 6155077 + 0 2 chr1 6467515 6475153 + 0 3 chr10 3640896 3649670 + 0 4 chr12 8400648 8405126 - 0 Expected Chromosome Start End Strand Distance 0 chr1 5703039 5707171 + 0 1 chr1 6149086 6155077 + 0 2 chr1 6467515 6475153 + 0 3 chr10 3640896 3649670 + 0 4 chr12 8400648 8405126 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplw7bytmh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplw7bytmh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsw8rh23h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsw8rh23h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvdbwlwo4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvdbwlwo4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps4cd1f8r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps4cd1f8r/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3_vcob5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3_vcob5a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7gej_n_c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7gej_n_c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfrj_dbq_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfrj_dbq_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvysy6nyh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvysy6nyh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd70n12na/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd70n12na/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp663cghlx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp663cghlx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9_p98lyy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_p98lyy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp65qm8v31/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp65qm8v31/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6fkbkvpg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6fkbkvpg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp53fk6opl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp53fk6opl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp76mcwuqs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp76mcwuqs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw5dyik_k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw5dyik_k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprv7_8wby/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprv7_8wby/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl_lp6fz6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl_lp6fz6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpash1j9t1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpash1j9t1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkl9c_zph/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkl9c_zph/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp0_snys2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp0_snys2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1rpfbc1s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1rpfbc1s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2i55sv4_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2i55sv4_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjw9kfcou/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjw9kfcou/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc2xs6b3o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc2xs6b3o/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5eqd8h2f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5eqd8h2f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp63n3o39d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp63n3o39d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2g8pl4rk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2g8pl4rk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeio0ivty/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeio0ivty/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpscjck16o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpscjck16o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4l903vns/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4l903vns/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6ipxvcth/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ipxvcth/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp9a_hmea/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp9a_hmea/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9pg4_sv2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9pg4_sv2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpepj4r91i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpepj4r91i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiij9riuc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiij9riuc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphkou8c6z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphkou8c6z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiofhd9_g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiofhd9_g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd6b4v4ql/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd6b4v4ql/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp67wm0c_j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp67wm0c_j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgrdsugs5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgrdsugs5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq3ljo7d3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq3ljo7d3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkhg2jho_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkhg2jho_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxt5mxck0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxt5mxck0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpygcnifrs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpygcnifrs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp445ins0x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp445ins0x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpho15vd_p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpho15vd_p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2t42mpzz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2t42mpzz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmvkanm2b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmvkanm2b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpglpb9bwn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpglpb9bwn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdcbdu7v4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdcbdu7v4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx933gefv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx933gefv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1eshkbn0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1eshkbn0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptp42iu9h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptp42iu9h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwk7q36nt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwk7q36nt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx6g3ycn0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx6g3ycn0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjn612czx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjn612czx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8lnofddr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8lnofddr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq264ebw0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq264ebw0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn32_c49z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn32_c49z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9b39cwge/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9b39cwge/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyb_g9am4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyb_g9am4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7bws1a7w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7bws1a7w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpttvjviyt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpttvjviyt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi48pbmzc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi48pbmzc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqoig879k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqoig879k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw815t0di/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw815t0di/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprjlup0_y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprjlup0_y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5fzoomsm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5fzoomsm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuog32wek/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuog32wek/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmvd2xp2u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmvd2xp2u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6ykoyak0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ykoyak0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6wdbzoh5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6wdbzoh5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2e2ixii7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2e2ixii7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc_jnozf3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc_jnozf3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpozerib07/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpozerib07/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpazibs8r6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpazibs8r6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1xndgw53/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1xndgw53/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9pgd4qzw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9pgd4qzw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiyi3vqlu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiyi3vqlu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3l0vavqj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3l0vavqj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1sjgaqaq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1sjgaqaq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprn5pgcgl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprn5pgcgl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp28xl6w6l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp28xl6w6l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpts0ku_3q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpts0ku_3q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcxecrj7c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcxecrj7c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjvqzpema/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjvqzpema/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppslqmra6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppslqmra6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_vcgpy2w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_vcgpy2w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr9qfe5uq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr9qfe5uq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpter4dr8n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpter4dr8n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzy9extwe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzy9extwe/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptmwqnil2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptmwqnil2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6rezy1c3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6rezy1c3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3_ssoqsc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3_ssoqsc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo7hie2zp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo7hie2zp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbk4tw46p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbk4tw46p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9oa02kss/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9oa02kss/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdcq5d3l2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdcq5d3l2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvsmodwv1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvsmodwv1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmigcqkp3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmigcqkp3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdtkr6sqq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdtkr6sqq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpidt1e700/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpidt1e700/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2izmbglm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2izmbglm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd6hlpkfb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd6hlpkfb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptkp_w8k7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptkp_w8k7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk2dvxbnn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk2dvxbnn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptczzk19m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptczzk19m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp41_keeyt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp41_keeyt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5jlt5nr3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5jlt5nr3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnkwjx9q2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnkwjx9q2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf6jlbdbq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf6jlbdbq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6odfjpqw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6odfjpqw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp21cdcvbq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp21cdcvbq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp258szsc3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp258szsc3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpte8sx4a_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpte8sx4a_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5ot8im7h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ot8im7h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfklo5zpx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfklo5zpx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm8dgqo6s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm8dgqo6s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4sw_06eb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4sw_06eb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptkt3gr8f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptkt3gr8f/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_fgbx1zh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_fgbx1zh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 665 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 665 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 665 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 665 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 665 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 665 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4asnogdw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4asnogdw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnsf9n_3o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnsf9n_3o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppdc7gzgk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppdc7gzgk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 665 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 665 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 665 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 665 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 665 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 665 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmzce7way/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmzce7way/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzj4rk4cm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzj4rk4cm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7i3vobpz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7i3vobpz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpviupu1p8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpviupu1p8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw7ska6is/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw7ska6is/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp1k7r8ij/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp1k7r8ij/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl03hup9p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl03hup9p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy5cwcvog/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy5cwcvog/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplchau0lq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplchau0lq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 665 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 665 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 665 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 665 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 665 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 665 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4czz0xgx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4czz0xgx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9yp4d_mh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9yp4d_mh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiqzj3jp_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiqzj3jp_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkl352nbg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkl352nbg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyntqn6x7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyntqn6x7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp95hro1e5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp95hro1e5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4uk_4pfo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4uk_4pfo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkg8jgt_s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkg8jgt_s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0q7z1msp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0q7z1msp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppso9zcql/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppso9zcql/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptd5gfssi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptd5gfssi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx7lagy_f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx7lagy_f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpneor4gx9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpneor4gx9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbrj344x5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbrj344x5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmynac3re/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmynac3re/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmo04l83q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmo04l83q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3wpv0t1k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3wpv0t1k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxlganicp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxlganicp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp65hw6tro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp65hw6tro/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplkeh6x7y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplkeh6x7y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuf7zzma7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuf7zzma7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbichsln6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbichsln6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpba3ram90/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpba3ram90/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplr0jqayn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplr0jqayn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp98drb2sp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp98drb2sp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ___________ test_three_in_a_row[strandedness_chain80-method_chain80] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2404778 | 2407025 | a | 0 | - | E | chr1 | 4238877 | 4246071 | a | 0 | - | E | chr1 | 8178473 | 8185952 | a | 0 | - | E | chr1 | 419038 | 419100 | a | 0 | - | E | ... | ... | ... | ... | ... | ... | E | chr16 | 8682989 | 8682990 | a | 0 | - | E | chr20 | 3596683 | 3604100 | a | 0 | + | E | chr20 | 620581 | 626247 | a | 0 | - | E | chr22 | 4732981 | 4740524 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 4238877 | 4246071 | a | 0 | - | E | chr1 | 8178473 | 8180621 | a | 0 | - | E | chr1 | 419038 | 419100 | a | 0 | - | E | chr1 | 2933371 | 2941628 | a | 0 | - | E | ... | ... | ... | ... | ... | ... | E | chr16 | 8682989 | 8690468 | a | 0 | - | E | chr20 | 3596683 | 3604100 | a | 0 | - | E | chr20 | 620581 | 626247 | a | 0 | - | E | chr22 | 4732981 | 4740524 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 6975712 | 6981891 | a | 0 | + | E | chr1 | 6975712 | 6984080 | a | 0 | - | E | chr1 | 6975712 | 6978841 | a | 0 | - | E | chr1 | 6975712 | 6982641 | a | 0 | - | E | chr1 | 6975712 | 6981429 | a | 0 | - | E | chr10 | 6975712 | 6978213 | a | 0 | + | E | chr13 | 6975712 | 6983209 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 7 rows and 6 columns from 3 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 32 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'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') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain100-method_chain100] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 176 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain111-method_chain111] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain137-method_chain137] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ___________ test_three_in_a_row[strandedness_chain72-method_chain72] ___________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') _________________________ test_nearest[None-True-same] _________________________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 123 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQEQA4qQMW') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | ~~~~~~~~~~~~~~~~~~~^ | lcol, | ^^^^^ | ...<12 lines>... | check_flags=False, | ^^^^^^^^^^^^^^^^^^ | ) | ^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness='same', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 459 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2scfmztg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2scfmztg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphyfmn2cx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphyfmn2cx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_wvw18qk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_wvw18qk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwtisxq0j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwtisxq0j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpennp8g85/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpennp8g85/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpysdwx3du/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpysdwx3du/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpowl6ctsw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpowl6ctsw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4q9h34i_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4q9h34i_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptvl34aop/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptvl34aop/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsow6f2cf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsow6f2cf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu6szfkmn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu6szfkmn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5qlqor_w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5qlqor_w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfystkukc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfystkukc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdf87cp42/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdf87cp42/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoyt4z3zm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoyt4z3zm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphw5p3y1o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphw5p3y1o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp59mwm8a3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp59mwm8a3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg1r7_uvh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg1r7_uvh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp6_tm74h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp6_tm74h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3i47wuvf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3i47wuvf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwtfubojp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwtfubojp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz3vqogh_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz3vqogh_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf9w_jtqu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf9w_jtqu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpch1dr8fw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpch1dr8fw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnn8nirhl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnn8nirhl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfrxlg9dm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfrxlg9dm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9mjxr4zp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9mjxr4zp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj7l7khvv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj7l7khvv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgbny35jl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgbny35jl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp816ojy9m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp816ojy9m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp00_44mg3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00_44mg3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsfi774vz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsfi774vz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy2nnho9u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy2nnho9u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnig3_7m5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnig3_7m5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvcerlupp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvcerlupp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdeaqj2en/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdeaqj2en/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp85jbm_j9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp85jbm_j9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbu07irv_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbu07irv_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwi3vorob/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwi3vorob/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0_pzcthe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_pzcthe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxpn7hrtw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxpn7hrtw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphgwurbm4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphgwurbm4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphdsc19m3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphdsc19m3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuvgwr2ym/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuvgwr2ym/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplesie_9b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplesie_9b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqbs2f7us/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqbs2f7us/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaxgtp2ik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaxgtp2ik/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv5v9wg57/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv5v9wg57/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkxttkzpb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkxttkzpb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgd2cuhxu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgd2cuhxu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprwneo2mp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprwneo2mp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjszt5325/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjszt5325/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4l_0r4m3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4l_0r4m3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx9m69qva/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9m69qva/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjrq8jnas/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjrq8jnas/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw9b0o1yg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw9b0o1yg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmperff988e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmperff988e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp76__17v6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp76__17v6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz3nsmzzm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz3nsmzzm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo7lmrwh_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo7lmrwh_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp43w3no5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp43w3no5a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5obop992/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5obop992/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdkdxz0gy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdkdxz0gy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyd_v6n14/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyd_v6n14/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpstaxz28k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpstaxz28k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp33b8n_oc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp33b8n_oc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbvrnjmi5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbvrnjmi5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg7_qxe3n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7_qxe3n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpim42036u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpim42036u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7bm71aro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7bm71aro/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1nmqjoiz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1nmqjoiz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5j5m5r45/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5j5m5r45/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdfvhwx9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdfvhwx9w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1ty7qsdg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ty7qsdg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1didb64n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1didb64n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyymry_ob/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyymry_ob/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuqwb3czh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuqwb3czh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpff3p_rfi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpff3p_rfi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpimrl02yj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpimrl02yj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbezpcf1o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbezpcf1o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnwtdi7ky/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnwtdi7ky/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1h284eok/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1h284eok/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjcfd5a_v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjcfd5a_v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjbyr5hbq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjbyr5hbq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7wkajbz6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7wkajbz6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3wkzriwy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3wkzriwy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpou61_o5r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpou61_o5r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc78uj3d_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc78uj3d_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwjyi44kl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwjyi44kl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfn5ge6zc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfn5ge6zc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9qk9s8sm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qk9s8sm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2pd03vdi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2pd03vdi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ae9edug/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ae9edug/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2f95p0fd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2f95p0fd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph2lkhvxk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph2lkhvxk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplm68r9ot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplm68r9ot/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpswv2vex1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpswv2vex1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkrek42c9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkrek42c9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp65gmnnk_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp65gmnnk_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpay69hcn3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpay69hcn3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkjxc7z02/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkjxc7z02/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4u3efsz4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4u3efsz4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7vabdq7k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7vabdq7k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7244 7245 + 0 1 chr1 7244 7245 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7244 | 7245 | a | 0 | ... | | chr1 | 7244 | 7245 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 7244 7245 + 0 1 chr1 7244 7245 + 0 df2 Chromosome Start End Strand Distance 0 chr1 7244 7245 + 0 1 chr1 7244 7245 + 0 Actual Chromosome Start End Strand Distance 0 chr1 7244 7245 + 0 1 chr1 7244 7245 + 0 Expected Chromosome Start End Strand Distance 0 chr1 7244 7245 + 0 1 chr1 7244 7245 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb_3try2q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb_3try2q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe_mf61nq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe_mf61nq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppff8rxjh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppff8rxjh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfc_e43tc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfc_e43tc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp029oejti/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp029oejti/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe9xtsp6r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe9xtsp6r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp79zi2sy1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp79zi2sy1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfovuwmzk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfovuwmzk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmfmt_ciq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmfmt_ciq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp41b48o11/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp41b48o11/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4l8p3ukb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4l8p3ukb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpghsdlj2r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpghsdlj2r/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcpagvv3k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcpagvv3k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1q8h521c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1q8h521c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplm856565/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplm856565/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz07r29zh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz07r29zh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplnwlx074/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplnwlx074/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjj6lpc_d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjj6lpc_d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsgswimwb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsgswimwb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplpgehzao/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplpgehzao/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpye8tncds/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpye8tncds/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] _____________________ test_nearest[downstream-False-False] _____________________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.End) | ^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=False, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:118 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGMEijDDEAAAx1ALW') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.Start, ocdf.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_ends.values - 1, right_starts.values, right_indexes) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=False, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:115 | (and 39 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3Qucl/DwODICEMMjEASmQ8AVaMD+w==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5nufq2qp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5nufq2qp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0czne1wj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0czne1wj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp74d1tv8c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp74d1tv8c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5mg7sxoo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5mg7sxoo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmzrv4_00/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmzrv4_00/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_efn5ujc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_efn5ujc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_9ga2gzq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_9ga2gzq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpep7_be7a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpep7_be7a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp040z5ipo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp040z5ipo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2lh48ap2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2lh48ap2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppjrrlo3a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppjrrlo3a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsvebjmuk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsvebjmuk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpigpwnp9r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpigpwnp9r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr7_sf90y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr7_sf90y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6n8lbe7i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6n8lbe7i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt9f4mkq7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt9f4mkq7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsiz09j0h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsiz09j0h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf3vu7_i4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf3vu7_i4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8pgj2abg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8pgj2abg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5ml5sl42/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ml5sl42/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprxzrayom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprxzrayom/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgyzx0vlp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgyzx0vlp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmkgs0d6m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmkgs0d6m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp869ytvs4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp869ytvs4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjwzgc7v1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjwzgc7v1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplovrnzoo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplovrnzoo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxhoruhxb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxhoruhxb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpillzg93g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpillzg93g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnwnqzqku/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnwnqzqku/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd40gmtz7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd40gmtz7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5qngarz4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5qngarz4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmdyz6e59/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmdyz6e59/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmwe_mljo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmwe_mljo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1e9yl0vr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1e9yl0vr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpycun1_tv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpycun1_tv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps9xlsrnb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps9xlsrnb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwem0ghki/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwem0ghki/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn_hds6rw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn_hds6rw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4g5_d7rm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4g5_d7rm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp11hnuk_t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp11hnuk_t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1c_h8xt6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1c_h8xt6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2g1slos_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2g1slos_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd4jjr2sm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd4jjr2sm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1tu6khzr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1tu6khzr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp93izwk2c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp93izwk2c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjawctj5p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjawctj5p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw4p90ibo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw4p90ibo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbwr5qnmv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbwr5qnmv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpplq81ii8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpplq81ii8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqe942syv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqe942syv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg3cbrrd_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg3cbrrd_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqdvgxjru/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqdvgxjru/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpysferrsu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpysferrsu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd38i6i37/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd38i6i37/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo5v2nbkx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo5v2nbkx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9dfuvh61/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9dfuvh61/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplf0g30dn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplf0g30dn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfo2txz84/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfo2txz84/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4tqk8yzx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4tqk8yzx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj1bxbiuf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj1bxbiuf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmpkhedjj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmpkhedjj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdc0bh2tp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdc0bh2tp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpczoh83h9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpczoh83h9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcma0mvms/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcma0mvms/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjo0u7m0b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjo0u7m0b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq51fvyxs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq51fvyxs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa1xwf2vl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa1xwf2vl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpucnpk6hg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpucnpk6hg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7mfesj5w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7mfesj5w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5lh3dvvk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5lh3dvvk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoa2gpqbx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoa2gpqbx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkvui0j9o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkvui0j9o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx7swzel_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx7swzel_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6s6r8l7t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6s6r8l7t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7yzyxf10/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7yzyxf10/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcqsbyt9s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcqsbyt9s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1wqpbz0z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1wqpbz0z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5nvb6xc0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5nvb6xc0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg71dmphb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg71dmphb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppm2rq5jo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppm2rq5jo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcajl6_f5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcajl6_f5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsjbyb_uf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsjbyb_uf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5yk4bnju/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5yk4bnju/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgwmms92p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgwmms92p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgdwcc8ys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgdwcc8ys/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnxqwt3fe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnxqwt3fe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjmz28rsu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjmz28rsu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe1s0drro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe1s0drro/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1w5zkjfa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1w5zkjfa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ur4xvc8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ur4xvc8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpftj6s1ps/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpftj6s1ps/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkdsvt82f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkdsvt82f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfyc6fqcr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfyc6fqcr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpio77kqd0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpio77kqd0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2oh3jtpl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2oh3jtpl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpse9p8pxb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpse9p8pxb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcf7ty5hi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcf7ty5hi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt4k2x1br/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt4k2x1br/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp4g7e1u1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp4g7e1u1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpej84z4zf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpej84z4zf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9yfq8wft/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9yfq8wft/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3r6r4crs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3r6r4crs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2asjvmj6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2asjvmj6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp35pf2c0s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp35pf2c0s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8kq13wuk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8kq13wuk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpangn87vj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpangn87vj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt2681now/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt2681now/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfscb5rgn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfscb5rgn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbd8c37e_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbd8c37e_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm08uh81o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm08uh81o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfm1vjfh0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfm1vjfh0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3mygxbaf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3mygxbaf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph4dmbdcs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph4dmbdcs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp98i6n7nt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp98i6n7nt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl_2lf8zu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl_2lf8zu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsllzs2jk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsllzs2jk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw4llnt7v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw4llnt7v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpifwbovae/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpifwbovae/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyb6e8ysv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyb6e8ysv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi7nda98i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi7nda98i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvhi4sxvd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvhi4sxvd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2614or9t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2614or9t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp28jcg_dy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp28jcg_dy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp91s96gph/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp91s96gph/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuffnknn3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuffnknn3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa_oek5zm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_oek5zm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8u8s7rdw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8u8s7rdw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm0b9ck99/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm0b9ck99/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6wdth1bs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6wdth1bs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp93nac51v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp93nac51v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppcqzotlg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppcqzotlg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmparwylw69/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmparwylw69/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsh52lzcq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsh52lzcq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcdk09c_6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcdk09c_6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk_y0581j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_y0581j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp75c3b77s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp75c3b77s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp795wkjux/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp795wkjux/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn7ff07g4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn7ff07g4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprv73thpa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprv73thpa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzckk2yew/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzckk2yew/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_wqndmv2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_wqndmv2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr9j9fm_4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr9j9fm_4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx5io47zx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx5io47zx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp59hazhhc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp59hazhhc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo7scb1jt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo7scb1jt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp62usyxe6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp62usyxe6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4f2ksaqk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4f2ksaqk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7g1i797z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7g1i797z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi7qeh2_f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi7qeh2_f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuuap5mlj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuuap5mlj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbhtnd8m5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbhtnd8m5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnam56m57/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnam56m57/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5jcntpos/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5jcntpos/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpydum6eza/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpydum6eza/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzs5mjq5x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzs5mjq5x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphyxiafm3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphyxiafm3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz34f0ld9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz34f0ld9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5nrqggrv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5nrqggrv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2usln_wi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2usln_wi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_misw8ax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_misw8ax/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcei6f4r6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcei6f4r6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgn1at5hy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgn1at5hy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj3h1y0_k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj3h1y0_k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp763k3o77/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp763k3o77/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1q77cu8j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1q77cu8j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplpptpkr6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplpptpkr6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf1jweii8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf1jweii8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbhvqvflz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbhvqvflz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn15ieddr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn15ieddr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwt9jbmgu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwt9jbmgu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp95o0mdys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp95o0mdys/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgclkfjts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgclkfjts/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf4ufsqvi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf4ufsqvi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8at2idzx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8at2idzx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2thsx2go/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2thsx2go/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp00wwm7q7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00wwm7q7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5imv5pcg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5imv5pcg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmw1d5361/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmw1d5361/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsk4nbc74/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsk4nbc74/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppzmsqdec/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppzmsqdec/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppy9bzbo2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppy9bzbo2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv_3ybmn0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv_3ybmn0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgdd_kngh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgdd_kngh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmrdajfl8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmrdajfl8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqbwsqiwr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqbwsqiwr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8x9tm1ui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8x9tm1ui/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6b1bmn37/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6b1bmn37/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp68tyk5pz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp68tyk5pz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqdhh2xi1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqdhh2xi1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplcux89ws/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplcux89ws/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdbd68r75/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdbd68r75/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzrzbf03e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzrzbf03e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp47ahjl2z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp47ahjl2z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3d1rtlfu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3d1rtlfu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpus8zyato/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpus8zyato/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9rl5xk9l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9rl5xk9l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp81aqzj7o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp81aqzj7o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4ai1otd8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ai1otd8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6ftbqeig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ftbqeig/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_9vwiljq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_9vwiljq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl6ixlml2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6ixlml2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4rzhf097/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4rzhf097/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzrqgchcg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzrqgchcg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz_vhsr10/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz_vhsr10/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7mgjre5s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7mgjre5s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvaaw0vpd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvaaw0vpd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk6gal30k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk6gal30k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfioxzyhy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfioxzyhy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpop6_b0kq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpop6_b0kq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5nlol4rj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5nlol4rj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvg5rwttr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvg5rwttr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbeae339n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbeae339n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprer86kap/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprer86kap/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdxjg5_hl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdxjg5_hl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqa6190_r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqa6190_r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph_94mjvq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph_94mjvq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplycnlpj4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplycnlpj4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe_cd8a39/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe_cd8a39/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2ca1ommf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ca1ommf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2gr9gyx6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2gr9gyx6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1j7v3hy8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1j7v3hy8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc2fvc5mr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc2fvc5mr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp77k1u8bl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp77k1u8bl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3zpiuxg2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3zpiuxg2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmping1mgo9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmping1mgo9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphj4zgixf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphj4zgixf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpupexckdy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpupexckdy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpizak4yrv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpizak4yrv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplkobwxm1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplkobwxm1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxtspl4pa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxtspl4pa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw80n95bp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw80n95bp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpslhfwry6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpslhfwry6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppco1maaf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppco1maaf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpojkeekim/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpojkeekim/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2r32p3x0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2r32p3x0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmposc_co_u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmposc_co_u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphpmevx8k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphpmevx8k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfw6og6es/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfw6og6es/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpze7hfptg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpze7hfptg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9hjxihxx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9hjxihxx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2xvxq4a9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2xvxq4a9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8uugxqdx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8uugxqdx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp20u18iju/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp20u18iju/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxh8qzf6h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxh8qzf6h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2qilpsbh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2qilpsbh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp28a12ogl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp28a12ogl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpftm3ppgp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpftm3ppgp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_l0py4ze/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_l0py4ze/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoqcoxuff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoqcoxuff/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8sf3jesn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8sf3jesn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv5lmooyv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv5lmooyv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppwdmfxj7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppwdmfxj7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp32_dhd8p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp32_dhd8p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf4ppr317/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf4ppr317/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx9ol2gdy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9ol2gdy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5qa6bj4m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5qa6bj4m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplvowg4vx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplvowg4vx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2d7gzgvw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2d7gzgvw/f2.bed) ________________ test_k_nearest[downstream-True-opposite-last] _________________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1e.values, d2s.values, d1e.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=True, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjRRRgBOKMDFg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1s.values, d2e.values, d1s.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=True, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 39 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGMEijDDEAAAx1ALW') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpncqzcz9h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpncqzcz9h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6il9ut3r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6il9ut3r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7myh5lk6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7myh5lk6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnrcpw35_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnrcpw35_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsl0d9hkj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsl0d9hkj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6mny_4v6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6mny_4v6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1r7utnmh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1r7utnmh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsw5sm42d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsw5sm42d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpypf50my2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpypf50my2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpywaeh0qm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpywaeh0qm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx9_3gcbl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9_3gcbl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp92d4l_ev/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp92d4l_ev/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptm_ovlvh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptm_ovlvh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc9vn9bhm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc9vn9bhm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxmrhu1de/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxmrhu1de/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsk99iu1v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsk99iu1v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9_o4pk1v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_o4pk1v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp68cid9xp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp68cid9xp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptq60h951/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptq60h951/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3whtd2gc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3whtd2gc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9rmu1vs6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9rmu1vs6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9fzjw2bv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9fzjw2bv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyjn02akw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyjn02akw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp86nnl5o6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp86nnl5o6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9zwws3s1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9zwws3s1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1q6kgwly/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1q6kgwly/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3jnzd1v5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3jnzd1v5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyl71p7ys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyl71p7ys/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvta9wwd3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvta9wwd3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps2loywk4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps2loywk4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1us_lb_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1us_lb_x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4zxc1h4m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4zxc1h4m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3a5gygxk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3a5gygxk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7agc45bd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7agc45bd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu8v7hea8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu8v7hea8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl_yvyypd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl_yvyypd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp532j6gqh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp532j6gqh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdbnmc286/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdbnmc286/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdjdssnmb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdjdssnmb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt6azuc6n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt6azuc6n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbrs3zrwe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbrs3zrwe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpylaye988/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpylaye988/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzslxdynv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzslxdynv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgzt0dafn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgzt0dafn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbvz201mo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbvz201mo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphe883yjn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphe883yjn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp46hn5jmi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp46hn5jmi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc0wkh4bk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc0wkh4bk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu4ykusnv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu4ykusnv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpleec68o1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpleec68o1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3vla19ka/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3vla19ka/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpintrybgi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpintrybgi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn379rvkw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn379rvkw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4d2j9m5j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4d2j9m5j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj31lqxjk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj31lqxjk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8044cygu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8044cygu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqv2vm8y2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqv2vm8y2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi8bbqgek/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi8bbqgek/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplstzy_go/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplstzy_go/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjqiwcwqs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjqiwcwqs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9tw055cc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9tw055cc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyi06uskv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyi06uskv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv4zuap4r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv4zuap4r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp45pz476l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp45pz476l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp606774xk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp606774xk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprmm95ljd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprmm95ljd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpizzgczw3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpizzgczw3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd8_gkwv0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd8_gkwv0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmcvhdhsn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmcvhdhsn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_0459gdr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_0459gdr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpumt3fczc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpumt3fczc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ox9_an9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ox9_an9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpijff0lgd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpijff0lgd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmph8f8ohys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph8f8ohys/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6n1_ymn7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6n1_ymn7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfq1as9sn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfq1as9sn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq84q08ih/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq84q08ih/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9ci77qui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ci77qui/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvoe58yk6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvoe58yk6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd01w2h6i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd01w2h6i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq9t64tk0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9t64tk0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6w__w5fh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6w__w5fh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpntxm5s6i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpntxm5s6i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpytn5w8fg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpytn5w8fg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkpzzzawy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkpzzzawy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp81icjdzj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp81icjdzj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdh3cunay/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdh3cunay/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj6fjre5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj6fjre5a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo8my1fzx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo8my1fzx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpep95rqn3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpep95rqn3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw_1q1qis/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw_1q1qis/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu4wwdd4h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu4wwdd4h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm5bi8se7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm5bi8se7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpag0pgwe0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpag0pgwe0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn386fxnx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn386fxnx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmph64gnkzl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph64gnkzl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_s2bg_67/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_s2bg_67/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr5r7j79e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr5r7j79e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxms9s0qj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxms9s0qj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzznuiqk6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzznuiqk6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp433jx3qu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp433jx3qu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzhwyu5o7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzhwyu5o7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiojcbacu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiojcbacu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoy3gjmg_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoy3gjmg_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptttl0spd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptttl0spd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp04tr12h4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp04tr12h4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxh5lv53l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxh5lv53l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi04va0r7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi04va0r7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4shwkkro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4shwkkro/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzm9j9a1b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzm9j9a1b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyurjlom5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyurjlom5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpothvpy7t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpothvpy7t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnmdyllc9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnmdyllc9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4v15ctu_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4v15ctu_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4gw0eykg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4gw0eykg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj1lnkmr5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj1lnkmr5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb_1ij4w3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb_1ij4w3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp_fuy3j1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_fuy3j1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6ghj7jh9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ghj7jh9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsqxzpsp8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsqxzpsp8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmper6ybdo5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmper6ybdo5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1iosnftp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1iosnftp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_5dwcdye/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_5dwcdye/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgkogqa4j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgkogqa4j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfbmk88ye/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfbmk88ye/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd0dus5en/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd0dus5en/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9sgww79i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9sgww79i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpljsvu013/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpljsvu013/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxlax6kdw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxlax6kdw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpob0bk2a2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpob0bk2a2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzt_n6zjn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzt_n6zjn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpokovo59f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpokovo59f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkx9sdw68/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkx9sdw68/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzc6h5aiz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzc6h5aiz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpamja_j_7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpamja_j_7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6yxjw2cw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6yxjw2cw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvi7v7d8b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvi7v7d8b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvl343i2d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvl343i2d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmxmiqdxf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmxmiqdxf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpilquigdz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpilquigdz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5mm20n94/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5mm20n94/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv9sj_eqx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv9sj_eqx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps3cq11s7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps3cq11s7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0oz31ulc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0oz31ulc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvvoyqwwo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvvoyqwwo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8w18o8bn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8w18o8bn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppgx8isf7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppgx8isf7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2bo_wqcr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2bo_wqcr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsn5_wosb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsn5_wosb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplvfxkp4c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplvfxkp4c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1v_zpn1k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1v_zpn1k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx6r2pms7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx6r2pms7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6ufzcu3p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ufzcu3p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbnueumo7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbnueumo7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprcx071c5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprcx071c5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppydomwfd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppydomwfd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy98_gl23/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy98_gl23/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8y8eqc53/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8y8eqc53/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkcwgdtok/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkcwgdtok/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp52q5r02i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp52q5r02i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphu4tvfys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphu4tvfys/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzkki8ros/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzkki8ros/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp712h_zfi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp712h_zfi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8emk582d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8emk582d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp584a0oqv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp584a0oqv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsv6_xl4s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsv6_xl4s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6_6pe629/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6_6pe629/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsxr7phdb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsxr7phdb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnlxp5vpu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnlxp5vpu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqum_x03m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqum_x03m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzamivq0c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzamivq0c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmjo5rs9m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmjo5rs9m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvwerdc0u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvwerdc0u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbvep6gui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbvep6gui/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc0mt5h_t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc0mt5h_t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpozbyrjwo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpozbyrjwo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn6bdpxej/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn6bdpxej/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppm9av_4c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppm9av_4c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcwluz80a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcwluz80a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzk6mpu9y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzk6mpu9y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppxcakqst/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppxcakqst/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvtn2fa9s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtn2fa9s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp22_p3hxu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp22_p3hxu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpagao20x3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpagao20x3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp04hqo95f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp04hqo95f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl3u12ftt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl3u12ftt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsq4fa8mo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsq4fa8mo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9bce0lng/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9bce0lng/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxrpsq5mn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxrpsq5mn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp9wrh4g_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp9wrh4g_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3cupo_it/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3cupo_it/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8g3onp_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8g3onp_h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpka4flpfi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpka4flpfi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1o3xlyuc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1o3xlyuc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptabjvzs7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptabjvzs7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpme9jzpq7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpme9jzpq7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpymigy35j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpymigy35j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeqcas9uh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeqcas9uh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpimtnuay7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpimtnuay7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsx_3hhk6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsx_3hhk6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp48cd4cq0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp48cd4cq0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc2htl9vu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc2htl9vu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3f8s9zc1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3f8s9zc1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpml7rydf_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpml7rydf_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppx5xvgap/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppx5xvgap/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptvd_x860/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptvd_x860/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb_78_ut4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb_78_ut4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk19ruihx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk19ruihx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcnz4zx_8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcnz4zx_8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbop4x1vb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbop4x1vb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkdujucpb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkdujucpb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbs4u9ozr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbs4u9ozr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptyuxkka3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptyuxkka3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpud6vidhe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpud6vidhe/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmn35lfjc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmn35lfjc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl8qicat1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl8qicat1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf3klupcz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf3klupcz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0tbxckn2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0tbxckn2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptqnkn1zu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptqnkn1zu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvmhjexwu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvmhjexwu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpixbcjabh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpixbcjabh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqf2bk9as/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqf2bk9as/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnpvv6j6q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnpvv6j6q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_a1bizro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_a1bizro/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2kp4q63y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2kp4q63y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw6935shi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw6935shi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5ecxrx7a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ecxrx7a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpycu6fner/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpycu6fner/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu4qu9sqo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu4qu9sqo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdlhl7ffj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdlhl7ffj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptup0u3b4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptup0u3b4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2d1wg08s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2d1wg08s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfh2nem0n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfh2nem0n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwg6n85uz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwg6n85uz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2i3uik8l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2i3uik8l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfmrghq56/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfmrghq56/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgfy3h1bc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgfy3h1bc/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain82-method_chain82] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2448950 | 2457150 | a | 0 | + | | chr1 | 5499597 | 5502819 | a | 0 | + | | chr1 | 6210051 | 6212991 | a | 0 | + | | chr8 | 2448950 | 2457016 | a | 0 | + | | chr18 | 2448950 | 2452577 | a | 0 | + | | chr20 | 2448950 | 2456704 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain101-method_chain101] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 178 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') _____________________ test_nearest[downstream-False-same] ______________________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 nearest_how = 'downstream', overlap = False, strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:115: in _nearest r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, pyranges/methods/nearest.py:62: in _next_nonoverlapping r_idx, dist = nearest_next_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E nearest_how='downstream', E overlap=False, E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E (and 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:34: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph_pdsdt1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph_pdsdt1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ercaroc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ercaroc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdauh7nac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdauh7nac/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn51m7lpi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn51m7lpi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplmwhkidj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplmwhkidj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8g2f_0q_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8g2f_0q_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8jx8fycf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8jx8fycf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdz4zjnuj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdz4zjnuj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7n8ctzd7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7n8ctzd7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphxmtgb2q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphxmtgb2q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_8f0sz7o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_8f0sz7o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjw0hy7vc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjw0hy7vc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2er25ad8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2er25ad8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7l174iwl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7l174iwl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplz1v6wm5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplz1v6wm5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprsdiqled/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprsdiqled/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfiqu83b6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfiqu83b6/f2.bed) __________ test_three_in_a_row[strandedness_chain138-method_chain138] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ___________ test_three_in_a_row[strandedness_chain27-method_chain27] ___________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGGEijECCCSEOhgwAZhcEYQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3091 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance, ... (+ 5 more.) ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') __________ test_three_in_a_row[strandedness_chain112-method_chain112] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/attr.py:65 E (and 176 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') _______________________ test_nearest[None-True-opposite] _______________________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 123 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGBEiTGARBgA4vAMX') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | ~~~~~~~~~~~~~~~~~~~^ | lcol, | ^^^^^ | ...<12 lines>... | check_flags=False, | ^^^^^^^^^^^^^^^^^^ | ) | ^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how=None, | overlap=True, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 455 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGMEijDDEAAAx1ALW') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdfgblny_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdfgblny_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprfkra869/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprfkra869/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4r55mkqp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4r55mkqp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjtetmcxg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjtetmcxg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzkf287kk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzkf287kk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8t42w2kz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8t42w2kz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7esi_97c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7esi_97c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8z7ivxld/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8z7ivxld/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9cw9sduw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9cw9sduw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmsawsyuv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmsawsyuv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpof3d3dlz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpof3d3dlz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe5gos7rk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe5gos7rk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprchn9bvs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprchn9bvs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2vwre3rs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2vwre3rs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv8z27vpt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv8z27vpt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf63p4_tv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf63p4_tv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo2upe4y8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo2upe4y8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 7987 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7987 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 7987 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 7987 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 7987 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 7987 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb1n766nq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb1n766nq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbh7c1hzu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbh7c1hzu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsqopej7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsqopej7q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ushfn_s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ushfn_s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvi7qfg20/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvi7qfg20/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgfr5t5p2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgfr5t5p2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdq4ac8nc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdq4ac8nc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpylbh7k1f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpylbh7k1f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwh1bz45e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwh1bz45e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpee83o8ln/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpee83o8ln/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwb6heo2q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwb6heo2q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmxhtnw44/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmxhtnw44/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpti9x_sso/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpti9x_sso/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3vqggdbb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3vqggdbb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprjcuhdt1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprjcuhdt1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_v3m6pk0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_v3m6pk0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8wkmhgpm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8wkmhgpm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmj2t88_9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmj2t88_9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp99qb5f46/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp99qb5f46/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi099tgn1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi099tgn1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpebwoy72i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpebwoy72i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp717psxj6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp717psxj6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0k8w0y27/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0k8w0y27/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1c6es9hd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1c6es9hd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpazs61hrq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpazs61hrq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl3lge4la/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl3lge4la/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr72ful1r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr72ful1r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3qytpue9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3qytpue9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0kghwnvr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0kghwnvr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcf3ocgw7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcf3ocgw7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplb_u5nw5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplb_u5nw5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdlotxpax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdlotxpax/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1aarq845/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1aarq845/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj7a5ejsw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj7a5ejsw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp260fo0b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp260fo0b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1d0fzr6o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1d0fzr6o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp64mods8e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp64mods8e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp890rcsl7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp890rcsl7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd_d1dsji/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd_d1dsji/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps_jqf3ii/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps_jqf3ii/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptsbnvqsu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptsbnvqsu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp15kvyvev/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp15kvyvev/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9h1_iwjs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9h1_iwjs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8ljzj109/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ljzj109/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7qghn5rt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qghn5rt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcovpjnw9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcovpjnw9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwqu0rpe8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwqu0rpe8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1uq274dk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1uq274dk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv6u8afdt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv6u8afdt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw7v4jhhs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw7v4jhhs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_e5up_qx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_e5up_qx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgtcub3w7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgtcub3w7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt6rx7mex/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt6rx7mex/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpery31w8w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpery31w8w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk80gguaw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk80gguaw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwp4wbvr0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwp4wbvr0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbcf2u_tn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbcf2u_tn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppba1wno3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppba1wno3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8c0lj5vr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8c0lj5vr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgloe9he7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgloe9he7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb0vz0u3o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb0vz0u3o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjho8uf0d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjho8uf0d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj8nk8tai/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj8nk8tai/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzl6jx46y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzl6jx46y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_s6puu_n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_s6puu_n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_h0f1c4d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_h0f1c4d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuh2e5ohy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuh2e5ohy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppqdwp_d9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppqdwp_d9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgq749lte/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgq749lte/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3yt_3wd5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3yt_3wd5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprgzc3h8n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprgzc3h8n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvzw2vxo5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvzw2vxo5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe8t0iamk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8t0iamk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw3jue09g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw3jue09g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbu0odb73/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbu0odb73/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc0weu9o5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc0weu9o5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdp9ngeb0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdp9ngeb0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjz538rot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjz538rot/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpou4adhi_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpou4adhi_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvntip9hl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvntip9hl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplo1ko4d1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplo1ko4d1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpur5_t2kc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpur5_t2kc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp377b8cz1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp377b8cz1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpixm4_ofw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpixm4_ofw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppwo1isqx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppwo1isqx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg18r59j_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg18r59j_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6zyc2yv7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6zyc2yv7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppou1f4aj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppou1f4aj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf_3jlgye/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf_3jlgye/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfiky5xyt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfiky5xyt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk6rj8frc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk6rj8frc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg7vcwumw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7vcwumw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqka9hm9j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqka9hm9j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwixoe1ky/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwixoe1ky/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg6arhxkh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg6arhxkh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9mzwq7dx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9mzwq7dx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyi1iqi0c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyi1iqi0c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph8rxwyd5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph8rxwyd5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvsihvjc2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvsihvjc2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjrifq64u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjrifq64u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5mgvb93c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5mgvb93c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgp095aog/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgp095aog/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr2k5skt4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr2k5skt4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc5du6qer/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc5du6qer/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnznzv013/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnznzv013/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwec4xfrr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwec4xfrr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4ljg7qy2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ljg7qy2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpweub62_l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpweub62_l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptv9v8zvi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptv9v8zvi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1qhjq4sm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1qhjq4sm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvzov4qg6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvzov4qg6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9883brp4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9883brp4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_855i3at/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_855i3at/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0s80fhwc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0s80fhwc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdchmdabu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdchmdabu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcu0dxs52/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcu0dxs52/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp14k1_o9p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp14k1_o9p/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzeq2mhhy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzeq2mhhy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkokvbym1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkokvbym1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4r4aa14p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4r4aa14p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5tpx5in1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5tpx5in1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9i8p8e4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9i8p8e4v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbkq0dyr3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbkq0dyr3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc6dwk0ls/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc6dwk0ls/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9qb8na7v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qb8na7v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6bjrar32/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6bjrar32/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7srg_hxl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7srg_hxl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn9em1k4f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn9em1k4f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpci38ttxq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpci38ttxq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpazesjccn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpazesjccn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0g9d2m2k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0g9d2m2k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfhyzhd_2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfhyzhd_2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3h46lsao/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3h46lsao/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp50ujwhcr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp50ujwhcr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp98emyxq7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp98emyxq7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgkds47i1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgkds47i1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3q5ifbnk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3q5ifbnk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpccrytbpe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpccrytbpe/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] __________ test_three_in_a_row[strandedness_chain123-method_chain123] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 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'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________________ test_nearest[downstream-False-opposite] ____________________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.Start, ocdf.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_ends.values - 1, right_starts.values, right_indexes) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=False, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 104 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjRRRgBOKMDFg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.End) | ^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='downstream', | overlap=False, | strandedness='opposite', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 103 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGMEijDDEAAAx1ALW') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjjzp8gm4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjjzp8gm4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9c54lgw6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9c54lgw6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph4n26lku/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph4n26lku/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv59ve2ii/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv59ve2ii/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgd4z68r3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgd4z68r3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmposmrqo4y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmposmrqo4y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpti1zw3c6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpti1zw3c6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps8pbn40t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps8pbn40t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5uhbk8mo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5uhbk8mo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9tbv0x7g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9tbv0x7g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6kjrue5e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6kjrue5e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq9u4vc16/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9u4vc16/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph3ecejyt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph3ecejyt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvbsgoksr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvbsgoksr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvk6rkias/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvk6rkias/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq6xnw_pl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq6xnw_pl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp504pl5d0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp504pl5d0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk3odzz13/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk3odzz13/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5ntdi7z9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ntdi7z9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6ax5wh5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ax5wh5c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmple6ag4we/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmple6ag4we/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpja0v6a1t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpja0v6a1t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpztgpqkeg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpztgpqkeg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq3k5ieo6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq3k5ieo6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph8w3qxif/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph8w3qxif/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqbtgemca/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqbtgemca/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz722i1vg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz722i1vg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpprpbtkp5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpprpbtkp5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl5_muna7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl5_muna7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi_pdldzb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi_pdldzb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_t7khsh8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_t7khsh8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvqhi7aws/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvqhi7aws/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoz4jn2z2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoz4jn2z2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptlorndqf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptlorndqf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3cloflch/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3cloflch/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4solrr8g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4solrr8g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp87xhtdrn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp87xhtdrn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplur84iah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplur84iah/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6hp87czf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6hp87czf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb5a4h1mo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb5a4h1mo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppcvr99l2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppcvr99l2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppthvl25r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppthvl25r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa9dt2tjw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa9dt2tjw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9a5wjzcq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9a5wjzcq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr5n_spz_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr5n_spz_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe7whzcev/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7whzcev/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5g1wycdm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5g1wycdm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc8ux9a26/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc8ux9a26/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_zklql6r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_zklql6r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy1kacu7b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy1kacu7b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp53bj7zg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp53bj7zg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4b5b37mo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4b5b37mo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4cejn4i4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4cejn4i4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjh66m0gq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjh66m0gq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmporo4u3dz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmporo4u3dz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4e57v5w3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4e57v5w3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptaxb4woo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptaxb4woo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp047snqtl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp047snqtl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkthoh9ak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkthoh9ak/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbom9t2gf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbom9t2gf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvwxzvnu8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvwxzvnu8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfd1lit8g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfd1lit8g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplpyirprq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplpyirprq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxwqa6fzr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxwqa6fzr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgpfwalz4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgpfwalz4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaaiqh6nb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaaiqh6nb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmlficpf3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmlficpf3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_4bay7m8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_4bay7m8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppxmrxsxv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppxmrxsxv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplm1vnxgr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplm1vnxgr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyqn2bie0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqn2bie0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp96k7jo4r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp96k7jo4r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl6c5s1z2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6c5s1z2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzy_jysrq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzy_jysrq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzsjufigo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzsjufigo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuhsbwy2y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuhsbwy2y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd2jemf25/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd2jemf25/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4slwzfol/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4slwzfol/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb7ogrtn8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb7ogrtn8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyu2hqt68/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyu2hqt68/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2z_zrki5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2z_zrki5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvznirpq7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvznirpq7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqyxx04un/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqyxx04un/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp23ka3gsw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp23ka3gsw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmza24oiz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmza24oiz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppb_ctcv9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppb_ctcv9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0a4o6u4h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0a4o6u4h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr8gg1nh5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr8gg1nh5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq9plja02/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9plja02/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1uyz9rxs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1uyz9rxs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8_yow8xz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8_yow8xz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpavch4z8n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpavch4z8n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptv2y75gt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptv2y75gt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpypu7m7om/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpypu7m7om/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_p_w3czr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_p_w3czr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp64g5664v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp64g5664v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfwjkxtye/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfwjkxtye/f2.bed) ________________________ test_nearest[None-False-False] ________________________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 nearest_how = None, overlap = False, strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E nearest_how=None, E overlap=False, E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:101 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E (and 33 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6sc68kpk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6sc68kpk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0qnkjyjy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0qnkjyjy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_cj893zq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_cj893zq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1vxvdcac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1vxvdcac/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2ml6ecz5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ml6ecz5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoqp451xs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoqp451xs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu5jwvn34/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu5jwvn34/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1s4hdw9f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1s4hdw9f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaom1vm31/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaom1vm31/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv7nazs3c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv7nazs3c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps_y7j3pn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps_y7j3pn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2lv25e37/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2lv25e37/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmhz2q_j3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmhz2q_j3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph00tpaep/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph00tpaep/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ijduc52/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ijduc52/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwbbeezb9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwbbeezb9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgpy6vksp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgpy6vksp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl611_v82/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl611_v82/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpztfz7w04/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpztfz7w04/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1v5g6n1g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1v5g6n1g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7qzu7anx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qzu7anx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5ia0z30n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ia0z30n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9hgz5ros/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9hgz5ros/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz3quxtvf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz3quxtvf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsq372f50/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsq372f50/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmb_8eu95/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmb_8eu95/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdplpsgef/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdplpsgef/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppmfep4di/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppmfep4di/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjsadt69c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjsadt69c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo5ry51nb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo5ry51nb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpps4h9kj7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpps4h9kj7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw29y7od2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw29y7od2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp343tqx0m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp343tqx0m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp20zo9c12/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp20zo9c12/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp64vrphff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp64vrphff/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoav13chy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoav13chy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4b40ktro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4b40ktro/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpumfswz6h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpumfswz6h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfqqyqbuk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfqqyqbuk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx6jz615k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx6jz615k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5n21rtr3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5n21rtr3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppjjwb4ct/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppjjwb4ct/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj3v7l1sk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj3v7l1sk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp517wkam7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp517wkam7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt9a7012e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt9a7012e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaktd831j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaktd831j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu2kd12sf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu2kd12sf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzf543rom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzf543rom/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp115qcfmb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp115qcfmb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzmy5acdb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzmy5acdb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpanxca9rf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpanxca9rf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk4q_2k2_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk4q_2k2_/f2.bed) __________ test_three_in_a_row[strandedness_chain102-method_chain102] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 182 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ________________________ test_nearest[None-False-same] _________________________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 nearest_how = None, overlap = False, strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E nearest_how=None, E overlap=False, E strandedness='same', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E (and 101 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpipi6xh4t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpipi6xh4t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2vxtcua7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2vxtcua7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxuaxy206/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxuaxy206/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz4rd5i3k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz4rd5i3k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmw54uoeq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmw54uoeq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpply66uwa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpply66uwa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppo8n1vc_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppo8n1vc_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcd9pmu02/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcd9pmu02/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzx22gegw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzx22gegw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl2kjotwc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl2kjotwc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps4d0wjs8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps4d0wjs8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmponndm_b7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmponndm_b7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr8x4ogao/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr8x4ogao/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn_h58mt1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn_h58mt1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5yi2btlm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5yi2btlm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr74oz0l3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr74oz0l3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg1rnwvo2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg1rnwvo2/f2.bed) __________ test_three_in_a_row[strandedness_chain139-method_chain139] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite'), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkdGQDYgZGR0YGBiCGIgYGACMIAlc=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ___________ test_three_in_a_row[strandedness_chain28-method_chain28] ___________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False), method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:21 E (and 142 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain113-method_chain113] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain73-method_chain73] ___________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ___________ test_three_in_a_row[strandedness_chain84-method_chain84] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E (and 130 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ______________________ test_nearest[None-False-opposite] _______________________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 nearest_how = None, overlap = False, strandedness = 'opposite' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E nearest_how=None, E overlap=False, E strandedness='opposite', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E (and 102 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjRRRgBOKMDFg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqtftezka/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqtftezka/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ds3e94v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ds3e94v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1czl7a0_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1czl7a0_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3dyejnxg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3dyejnxg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5799x5ld/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5799x5ld/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8n65f3tp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8n65f3tp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppegifmpa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppegifmpa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpprjmnjar/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpprjmnjar/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnyxdsjuw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnyxdsjuw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0sia18ee/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0sia18ee/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5qw_3obl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5qw_3obl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpru6nl1k3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpru6nl1k3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi5g1h7ju/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi5g1h7ju/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk80eey62/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk80eey62/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6qet69fd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6qet69fd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp04i6g64q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp04i6g64q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxqos90ok/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxqos90ok/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyjs9446y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyjs9446y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt49iqyql/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt49iqyql/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwa09q106/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwa09q106/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl90ui3dl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl90ui3dl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy2kgikql/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy2kgikql/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpticih7qh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpticih7qh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8tgkmn76/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8tgkmn76/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppacobh21/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppacobh21/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw0w7or52/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw0w7or52/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplg80iymo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplg80iymo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0e3bttbi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0e3bttbi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwvuy6lft/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwvuy6lft/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppia_8wn1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppia_8wn1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_acddfnc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_acddfnc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptanedk4s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptanedk4s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphkozula4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphkozula4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptci2mbf0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptci2mbf0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ak0wtpm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ak0wtpm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpagrbf9s3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpagrbf9s3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplfethjto/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplfethjto/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6xfizzo9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6xfizzo9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzjjmp1d8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzjjmp1d8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2clw39ul/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2clw39ul/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi8d3b2ys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi8d3b2ys/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxf97_lmm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxf97_lmm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_cp3khmi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_cp3khmi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3927e7uv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3927e7uv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj5qw5187/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5qw5187/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfug98hv6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfug98hv6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ibd4m6z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ibd4m6z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2ckmf7_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ckmf7_e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb_mgux1w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb_mgux1w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc9ux5_6_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc9ux5_6_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1m39x8ir/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1m39x8ir/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvwsbxbbf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvwsbxbbf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptme7mxst/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptme7mxst/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1fkjcr37/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1fkjcr37/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplcc5eeft/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplcc5eeft/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6fny_j8k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6fny_j8k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm7gaexj5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm7gaexj5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd8zry5hm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd8zry5hm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgl7hb90d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgl7hb90d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyiw_d5d4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyiw_d5d4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzepyizv5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzepyizv5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1b1fvpo_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1b1fvpo_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo9awaqhr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo9awaqhr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7jo5t129/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7jo5t129/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf__pqo2b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf__pqo2b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0o9io_hc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0o9io_hc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8qtyz60i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8qtyz60i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwdiiv4zh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwdiiv4zh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsme53bwh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsme53bwh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkkzxpflx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkkzxpflx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpswcboqql/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpswcboqql/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3ohtuvm8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ohtuvm8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_64b3tiv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_64b3tiv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0yr2o_s2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0yr2o_s2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7tiubmd0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7tiubmd0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpimcz6n34/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpimcz6n34/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp97rhkc5t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp97rhkc5t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxx4w44im/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxx4w44im/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphw7bfmt5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphw7bfmt5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphh2323je/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphh2323je/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr52o9t_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr52o9t_x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe8r38hv1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8r38hv1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2d8u3zc9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2d8u3zc9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd7jds1jt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd7jds1jt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2sjq_php/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2sjq_php/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8ptmupl5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ptmupl5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqw8jvhbe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqw8jvhbe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4t4x8xog/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4t4x8xog/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvl_tti3k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvl_tti3k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk7r72y_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk7r72y_x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsjnqxqby/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsjnqxqby/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe_74oxxk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe_74oxxk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu47qrve8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu47qrve8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp55ur74wl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp55ur74wl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmgj09i3r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmgj09i3r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx05659ut/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx05659ut/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp73_xtikr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp73_xtikr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpemrag3_u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpemrag3_u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoepehxkl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoepehxkl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjvaql58f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjvaql58f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpql2ufuue/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpql2ufuue/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmjdq46yp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmjdq46yp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1lo03wom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1lo03wom/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplgoqpl34/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplgoqpl34/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz1kr3i3c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz1kr3i3c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6qivf4lb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6qivf4lb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqi8964yi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqi8964yi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprqt9k3hq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprqt9k3hq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpomq7nu6_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpomq7nu6_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpagdd3ddy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpagdd3ddy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnvme8xjv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnvme8xjv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp35z12xwk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp35z12xwk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe6wn0h3y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe6wn0h3y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp99yjpcmy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp99yjpcmy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp060ua70c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp060ua70c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4rm30rg4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4rm30rg4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmponlz2vrz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmponlz2vrz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8nszda8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8nszda8_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjq2s_q2k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjq2s_q2k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi59c7bh0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi59c7bh0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp19yq6tzt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp19yq6tzt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp09f4osaj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp09f4osaj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp__b418g3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp__b418g3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcdqwy_qw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcdqwy_qw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphzgoblzc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphzgoblzc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplhcmfz2a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplhcmfz2a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps2tfs_4t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps2tfs_4t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2f2j1dw4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2f2j1dw4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp97z7f9dk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp97z7f9dk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj_5c58ld/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj_5c58ld/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpftaldtni/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpftaldtni/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmhm398_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmhm398_e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4y7wkrjy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4y7wkrjy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpusr6oc23/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpusr6oc23/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpak1iw85f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpak1iw85f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp58690cd2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp58690cd2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp13qrdmyr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp13qrdmyr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkh86uami/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkh86uami/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc089_ah8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc089_ah8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxqn1kat1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxqn1kat1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppa0s56kw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppa0s56kw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqgqtj_0y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqgqtj_0y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4pj6njaj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4pj6njaj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpezax90vi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpezax90vi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiic96jxp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiic96jxp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4z9p7hl2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4z9p7hl2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo041pe85/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo041pe85/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe7qf7qqz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7qf7qqz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphcakdglz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphcakdglz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5jks52jf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5jks52jf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz_ogy08_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz_ogy08_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpja0un12d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpja0un12d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8nhorz1i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8nhorz1i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkdgzhti2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkdgzhti2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxf6n11u8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxf6n11u8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv15owhph/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv15owhph/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2htim09e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2htim09e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv64g0et_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv64g0et_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf5tsp_nn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf5tsp_nn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpibdh8s9y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpibdh8s9y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt3xcaozz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt3xcaozz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgoogefat/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgoogefat/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmi7ejwv6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmi7ejwv6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplpjjjo8g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplpjjjo8g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa73_s35y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa73_s35y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsduggren/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsduggren/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo7g3ty0k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo7g3ty0k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8yu0t9j1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8yu0t9j1/f2.bed) __________ test_three_in_a_row[strandedness_chain103-method_chain103] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 117 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain140-method_chain140] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite'), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/attr.py:65 E (and 246 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ___________ test_three_in_a_row[strandedness_chain29-method_chain29] ___________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', False) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', False), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') __________________ test_k_nearest[downstream-True-same-last] ___________________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1s.values, d2e.values, d1s.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=True, | strandedness='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 5135433 | 5143588 | a | 0 | + | | | chr1 | 516310 | 517571 | a | 0 | + | | | chr1 | 9183499 | 9184569 | a | 0 | + | | | chr1 | 853010 | 862043 | a | 0 | + | | | ... | ... | ... | ... | ... | ... | | | chr18 | 5148412 | 5156884 | a | 0 | + | | | chr18 | 5148412 | 5156884 | a | 0 | - | | | chr18 | 3754089 | 3757859 | a | 0 | - | | | chr18 | 5148412 | 5156884 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 6858576 | 6865180 | a | 0 | - | | | chr2 | 4722137 | 4730526 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 39 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3SWlNZgdLYvncDozDc/j9FZRcSO0Tl2x3xGZ4Oos4wuDG3PnzE6i78TBEobmQD5Xa5bGZ1FNygyMDoyOzI48jE6sjoyAgkgl9GRHcQE0gwgyAhCTCARRjiXBc5iAKkRBNLOfjGeQCXO7A+uAY1xYeiM/ApU58zLIgRWx+Fs6ZHJCNXE7MLQspcPYrALQ48iN1B33x+gbieWt0ClTny7GMH2wRCTE4sejM3sJF4MNNhJGWgbg5P8baBlToyBDE6KEiB3M0DdyAIiYNbBvAD2K9AILpCrGRmd65n2MzrLr90HUQqzDsxgcM5YHgDyjgfvTZB2J8kzIL86KRyFGgt3G1A5AwDgREDa') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1e.values, d2s.values, d1e.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=True, | strandedness='same', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 40 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprptkacwo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprptkacwo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_3cq0klc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_3cq0klc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2n9cxgey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2n9cxgey/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcqwonjp6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcqwonjp6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9yic63v1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9yic63v1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpse8wi5qy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpse8wi5qy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmt1uj3hu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmt1uj3hu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4t4dour_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4t4dour_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuc0n9ows/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuc0n9ows/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdjb6bx5p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdjb6bx5p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqopsh396/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqopsh396/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkk75hhhv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkk75hhhv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp94h7miy_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp94h7miy_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkqrgryhr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkqrgryhr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoolnhv2s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoolnhv2s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd21b0lp0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd21b0lp0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp450jz8kp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp450jz8kp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpey5h40on/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpey5h40on/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp05epn2qw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp05epn2qw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoo44wy57/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoo44wy57/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp36nzolhz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36nzolhz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9f33xxzh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9f33xxzh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvlwjt3oy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvlwjt3oy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9vl3pne0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9vl3pne0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpabdmfxxe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpabdmfxxe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpevl0cr4l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpevl0cr4l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf76kwzlv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf76kwzlv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5t8bxn79/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5t8bxn79/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw6rtjgkc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw6rtjgkc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1cgw5fle/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1cgw5fle/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf7quuw0t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf7quuw0t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdlyj75_f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdlyj75_f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9szb3op3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9szb3op3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvdnz9_0l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvdnz9_0l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjoj20a86/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjoj20a86/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi3n4rsvb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi3n4rsvb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy40nxwla/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy40nxwla/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppl_10pae/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppl_10pae/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnxkng531/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnxkng531/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwllzcidu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwllzcidu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkj82hpdv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkj82hpdv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpouci0kyq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpouci0kyq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpytn9gqgu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpytn9gqgu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6lglaql_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6lglaql_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpekqteipj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpekqteipj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcjoq3na8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcjoq3na8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf286erc6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf286erc6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpruth4i34/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpruth4i34/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppp98mfsi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppp98mfsi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjusaen45/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjusaen45/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptcy79hv9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptcy79hv9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzh35fl9c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzh35fl9c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj9gaag5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj9gaag5d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiibe34yl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiibe34yl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqm4rvggl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqm4rvggl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp134xzopt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp134xzopt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy71l3kcg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy71l3kcg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7ju7v2bs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ju7v2bs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzh7wgjxv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzh7wgjxv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpraf6s6n2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpraf6s6n2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy7th884a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy7th884a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2r0_x00w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2r0_x00w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbij2ll5g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbij2ll5g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2iociznk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2iociznk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa0xchour/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa0xchour/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmhv94nad/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmhv94nad/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbbh3_jxy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbbh3_jxy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx6rvz8sq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx6rvz8sq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyiz2_ats/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyiz2_ats/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcmul54c6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcmul54c6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdbrp_g1y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdbrp_g1y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8p1i8cwn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8p1i8cwn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5n0yu6f_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5n0yu6f_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplp6prj_z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplp6prj_z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpch_c4abc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpch_c4abc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnhkxo1c5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnhkxo1c5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphb0fyxpy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphb0fyxpy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0a2hanlt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0a2hanlt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7dbsnm23/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7dbsnm23/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1b3wk28o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1b3wk28o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxqiyxcey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxqiyxcey/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn0e9puma/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn0e9puma/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf8g3lf5b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf8g3lf5b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvuacumz7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvuacumz7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7wpi0gf4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7wpi0gf4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt0l25fqm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt0l25fqm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmlhzp36q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmlhzp36q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxokw0k7e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxokw0k7e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp41d_3630/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp41d_3630/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe1xz_yx8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe1xz_yx8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprtyvfs32/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprtyvfs32/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp774jerm9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp774jerm9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjn1mxvln/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjn1mxvln/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzw68j1bk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzw68j1bk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprqg6lt2s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprqg6lt2s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpllv3i8ga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpllv3i8ga/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphtih87pq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphtih87pq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_vg55yg8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_vg55yg8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8knt46_t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8knt46_t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe6gjq10e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe6gjq10e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpedb747ig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpedb747ig/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnd1yak16/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnd1yak16/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpncfixixv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpncfixixv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp84dp1bbo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp84dp1bbo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgrzug87s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgrzug87s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9jhjl450/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9jhjl450/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzcd9zl2w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzcd9zl2w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmegmbean/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmegmbean/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcgnawntg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcgnawntg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4yrcwrfv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4yrcwrfv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv5dk4i11/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv5dk4i11/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmps1_vxj40/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps1_vxj40/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv7r_dzzn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv7r_dzzn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcvo3nyf1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcvo3nyf1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0l3ex7h_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0l3ex7h_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkepy8q59/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkepy8q59/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3vyvfct2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3vyvfct2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq1vq7of9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq1vq7of9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpohbaftb6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpohbaftb6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptkzpbep0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptkzpbep0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq62xc_ra/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq62xc_ra/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyduq7jgl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyduq7jgl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpih51885f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpih51885f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1r4y159e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1r4y159e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpow_4cf1r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpow_4cf1r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_ucmpfi5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ucmpfi5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp16e0ilgx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp16e0ilgx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuyzlj0rr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuyzlj0rr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp01rvec8d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp01rvec8d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr9ql4a04/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr9ql4a04/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpizpf3ild/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpizpf3ild/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpphn16r3l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpphn16r3l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo8s40tk4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo8s40tk4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy9sx42a2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy9sx42a2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7d_qkp68/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7d_qkp68/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmps7gs7z9m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps7gs7z9m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqwh3ugsq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqwh3ugsq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpryqguca3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpryqguca3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf0dqtydd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf0dqtydd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi2uzy_3m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi2uzy_3m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp93d400b_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp93d400b_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq0ovbqoz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq0ovbqoz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp36uxo1a0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36uxo1a0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsthsl5hv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsthsl5hv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3tntwi56/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3tntwi56/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpklwsd_lr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpklwsd_lr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc047q6s_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc047q6s_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxjy5crhw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxjy5crhw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyfwowv4d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyfwowv4d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprmeb5qmz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprmeb5qmz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpru80cnka/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpru80cnka/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptpoq733e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptpoq733e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplkmkjp2r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplkmkjp2r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprvscxvnb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprvscxvnb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz5fskjd7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz5fskjd7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8hjdkv89/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8hjdkv89/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9gawf5z4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9gawf5z4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9zr5c5dm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9zr5c5dm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz7jl1y_q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz7jl1y_q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeoxo25te/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeoxo25te/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsxkq4_ik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsxkq4_ik/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxsp89id2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxsp89id2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqnxs73yx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqnxs73yx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphg6a5hzk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphg6a5hzk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm6pg0ws6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm6pg0ws6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3kp8pv5m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3kp8pv5m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd698j9b_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd698j9b_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8czuf9xh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8czuf9xh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr3qiaij8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr3qiaij8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvsh8ss5f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvsh8ss5f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxf47e7kk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxf47e7kk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1qohvld5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1qohvld5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfmowgbpo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfmowgbpo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbdpmwe_u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbdpmwe_u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphzzp1vwg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphzzp1vwg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwlmznn12/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwlmznn12/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf2a61c0o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf2a61c0o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6uly54_r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6uly54_r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyv7bwn56/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyv7bwn56/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4vobk8wl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4vobk8wl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmtv9zreq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmtv9zreq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprk4ej8ra/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprk4ej8ra/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi3kn568t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi3kn568t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz7zwx_lk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz7zwx_lk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj0x8esy9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj0x8esy9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx3reo86o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3reo86o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_3a123t_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_3a123t_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7sa4be6m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7sa4be6m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0m0f44jl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0m0f44jl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz9000atd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz9000atd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfy2ri5xv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfy2ri5xv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb7ilw_7g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb7ilw_7g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3mzq67za/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3mzq67za/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplgujeecm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplgujeecm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptsib11v0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptsib11v0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjrdqack6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjrdqack6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphjxdy4jd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphjxdy4jd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe04ipox9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe04ipox9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpflh8jdpz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpflh8jdpz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplyn6fg0q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplyn6fg0q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1vro6bm3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1vro6bm3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7jujvz0s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7jujvz0s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxkz5ilrq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxkz5ilrq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo5kgpjtp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo5kgpjtp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo_vxgmi7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo_vxgmi7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwzcnrcqg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwzcnrcqg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg7gabzeh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7gabzeh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbjijaoo1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbjijaoo1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_4eegeq7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_4eegeq7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9c2le482/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9c2le482/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1gn9p6cu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1gn9p6cu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt8y7kofu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt8y7kofu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8x3g_ols/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8x3g_ols/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf4reqbyp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf4reqbyp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt_4o2ut9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt_4o2ut9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpocrbg8d_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpocrbg8d_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp_kmlw85/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_kmlw85/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmbv7m8hs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmbv7m8hs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaqzduchc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaqzduchc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2014xqz1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2014xqz1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7fv_jfxh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7fv_jfxh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp1tlfsd7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp1tlfsd7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz4tkw4bx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz4tkw4bx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl9_bq_e7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl9_bq_e7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5q5iiaax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5q5iiaax/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxsfo3dk7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxsfo3dk7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjf3dmfx_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjf3dmfx_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppronzyih/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppronzyih/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2iywzdcr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2iywzdcr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl0zysn07/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0zysn07/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8khf82cb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8khf82cb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplwdgw08p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplwdgw08p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprpsv_lij/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprpsv_lij/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpql7khf1p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpql7khf1p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_eo3qvuf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_eo3qvuf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6kuw866w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6kuw866w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyfpfh9dt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyfpfh9dt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcu08aibe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcu08aibe/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl9iporqt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl9iporqt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqd_gzo64/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqd_gzo64/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppylyyylf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppylyyylf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprcc2i7rl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprcc2i7rl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3w58vumv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3w58vumv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmph37fdihz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph37fdihz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpspdebmrg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpspdebmrg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4qik4q4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4qik4q4v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpef0ct9z1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpef0ct9z1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj_3yws1_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj_3yws1_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj5a3owqh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5a3owqh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpko3xvryl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpko3xvryl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcqpwpuwd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcqpwpuwd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpds1ncmih/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpds1ncmih/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptfcixsbb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptfcixsbb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn_5x8q34/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn_5x8q34/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzw2w5d14/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzw2w5d14/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsxiubs7p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsxiubs7p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1x3p3th8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1x3p3th8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp051t6ex7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp051t6ex7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9g7nehlr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9g7nehlr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcq1tok2h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcq1tok2h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1yzr4v5l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1yzr4v5l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpneaiew86/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpneaiew86/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7_p20kle/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7_p20kle/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz8vlm0dp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz8vlm0dp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiyzwxetb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiyzwxetb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxjr9u9n1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxjr9u9n1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppfohfs4p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppfohfs4p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu2o1aj16/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu2o1aj16/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzd34yrzo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzd34yrzo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4glxez0x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4glxez0x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkihokb77/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkihokb77/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwj6kgu09/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwj6kgu09/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnmu4b3rt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnmu4b3rt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyprebl92/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyprebl92/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_bzefzkb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_bzefzkb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm6d_3rxn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm6d_3rxn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv1aey9a_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv1aey9a_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5k6y51vx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5k6y51vx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppenayits/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppenayits/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt_stee1j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt_stee1j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz9fbxg90/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz9fbxg90/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4kt9guei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4kt9guei/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm8g8btxy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm8g8btxy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl9q8013d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl9q8013d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7_xmqu0k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7_xmqu0k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmps8w075ze/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps8w075ze/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmzvobaip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmzvobaip/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppk99avqe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppk99avqe/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6jslu6dv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6jslu6dv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr55afcen/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr55afcen/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphmt473w7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphmt473w7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpymefmpu5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpymefmpu5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8dwgb92m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8dwgb92m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppa2imouc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppa2imouc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp41yjf8wn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp41yjf8wn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjaihwoiu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjaihwoiu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzq43jlej/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzq43jlej/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprdaso_ac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprdaso_ac/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3cq7cprb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3cq7cprb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbpf1y5sp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbpf1y5sp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo2hhztwj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo2hhztwj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp01i15zn2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp01i15zn2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2l226m4p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2l226m4p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn28l6arv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn28l6arv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2cmqpyr7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2cmqpyr7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuw4v9seu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuw4v9seu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbslseuc1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbslseuc1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphp1ls1_k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphp1ls1_k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyw7caswq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyw7caswq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfs5kzjx1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfs5kzjx1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfen2ahbj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfen2ahbj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7063kf05/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7063kf05/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy3h65ru5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy3h65ru5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6kxngme_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6kxngme_/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain85-method_chain85] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same') method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E (and 117 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain141-method_chain141] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 75 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain104-method_chain104] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite'), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 183 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________________ test_k_nearest[downstream-True-False-last] __________________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1s.values, d2e.values, d1s.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=True, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:19 | (and 37 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGMEijDDEAAAx1ALW') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1e.values, d2s.values, d1e.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='downstream', | overlap=True, | strandedness=False, | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:42 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:46 | (and 37 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf6qr1w_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf6qr1w_e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy8puu8gh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy8puu8gh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2uxx8eds/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2uxx8eds/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkd7yxvf9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkd7yxvf9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3op5r6d2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3op5r6d2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl8x42vup/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl8x42vup/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp42gh698u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp42gh698u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0ra1x18s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ra1x18s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfcrilsmc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfcrilsmc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6g9d7s8a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6g9d7s8a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7dj_fk5t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7dj_fk5t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcfcetry1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcfcetry1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2z3f_wm5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2z3f_wm5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwfyml4pm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwfyml4pm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfa055vcu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfa055vcu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4pbnr67z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4pbnr67z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7_ksxf35/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7_ksxf35/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe8x303p2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8x303p2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptwejg4ba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptwejg4ba/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpby1g9d_n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpby1g9d_n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeyivwi1m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeyivwi1m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz9dr8o0o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz9dr8o0o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3954xz76/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3954xz76/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvjk0pps1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvjk0pps1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5n312_ir/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5n312_ir/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmprhck6lcg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprhck6lcg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpamcr4vn3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpamcr4vn3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmft1fkwm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmft1fkwm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbpfq9mo7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbpfq9mo7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_6euedkd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_6euedkd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjwoi3vho/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjwoi3vho/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcvj625z7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcvj625z7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgy50kng6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgy50kng6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdlyuig_c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdlyuig_c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjs4n8j4i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjs4n8j4i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyypmqfvq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyypmqfvq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvsntzy6k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvsntzy6k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4evzlpex/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4evzlpex/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_k70sl2e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_k70sl2e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp085htf1i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp085htf1i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv6iepaeh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv6iepaeh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz0c74o95/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz0c74o95/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxxb4vp57/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxxb4vp57/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzan6c7df/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzan6c7df/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2lphwxyx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2lphwxyx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnjpxf0js/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnjpxf0js/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm9xe_rop/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm9xe_rop/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuspzk4yj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuspzk4yj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk1t1phn5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk1t1phn5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0b_2s6nd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0b_2s6nd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2nrpxr6x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2nrpxr6x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0ak28jq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ak28jq2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbbljw1_l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbbljw1_l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw84pdd5j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw84pdd5j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0jsu7xd1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0jsu7xd1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptbc8gkjk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptbc8gkjk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmjn6n793/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmjn6n793/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw9kftdfm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw9kftdfm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp78zdl8qw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp78zdl8qw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr52dpdef/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr52dpdef/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzmx2ptqp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzmx2ptqp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr7q3ec7g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr7q3ec7g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf4dy4tj9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf4dy4tj9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp11ho9pus/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp11ho9pus/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5w6kru2c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5w6kru2c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeo9y_5_3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeo9y_5_3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdlee9zar/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdlee9zar/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi04kng_0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi04kng_0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcsma76iu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcsma76iu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr7m3iwvf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr7m3iwvf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpso9wu9nj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpso9wu9nj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzgmm9dyo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzgmm9dyo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnk33ics8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnk33ics8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb9m4i00r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb9m4i00r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmprbat479j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprbat479j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnliyrbom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnliyrbom/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8r_3o_yo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8r_3o_yo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa1jhb4mr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa1jhb4mr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi1lj667f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi1lj667f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg35bs28d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg35bs28d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy_am345g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy_am345g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9829_dvg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9829_dvg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptiwbo112/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptiwbo112/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq6vt3mer/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq6vt3mer/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc54i4czk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc54i4czk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdthh2_w4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdthh2_w4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnad_wiol/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnad_wiol/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0vm5zg91/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0vm5zg91/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmph1fv21vv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph1fv21vv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmppu9il98u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppu9il98u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptve7l6bj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptve7l6bj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6qs_ul3u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6qs_ul3u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgeitbay6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgeitbay6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4q_b57c9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4q_b57c9/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr16 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. __________ test_three_in_a_row[strandedness_chain175-method_chain175] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:21 E (and 142 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') _____________________________ test_jaccard[False] ______________________________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:363: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:378: in test_jaccard result = gr.stats.jaccard(gr2, strandedness=strandedness) pyranges/statistics.py:766: in jaccard for v in self.set_intersect(other).lengths(as_dict=True).values()) pyranges/pyranges.py:3687: in set_intersect self_clusters = self.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_jaccard( E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3Tmy9FjYHBkhCEGRiCJzAcAPtoDPg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception __________ test_three_in_a_row[strandedness_chain124-method_chain124] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3SO/biVgcGREYYYGIEkkHIEEkwQESAJhgwAo+IF4Q==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9705867 | 9708609 | a | 0 | ... | | chr1 | 6338777 | 6345355 | a | 0 | ... | | chr11 | 9705867 | 9711627 | a | 0 | ... | | chr21 | 9705867 | 9707796 | a | 0 | ... | | chrM | 9705867 | 9713328 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain74-method_chain74] ___________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGGEijECCCSEOhgwAZhcEYQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7690381 | 7696915 | a | 0 | ... | | chr1 | 2162461 | 2162650 | a | 0 | ... | | chr1 | 7400310 | 7404757 | a | 0 | ... | | chr1 | 3873991 | 3875835 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr11 | 8164873 | 8165700 | a | 0 | ... | | chr15 | 4864959 | 4874205 | a | 0 | ... | | chrM | 1829800 | 1832018 | a | 0 | ... | | chrX | 5279162 | 5281833 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 82863 | 89939 | a | 0 | ... | | chr1 | 1743658 | 1745494 | a | 0 | ... | | chr1 | 8761423 | 8763893 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr4 | 9599474 | 9600305 | a | 0 | ... | | chr4 | 5599654 | 5609596 | a | 0 | ... | | chr4 | 1900182 | 1900628 | a | 0 | ... | | chr4 | 4962441 | 4969660 | a | 0 | ... | | chr4 | 5166874 | 5169791 | a | 0 | ... | | chr4 | 8331851 | 8339050 | a | 0 | ... | | chr4 | 9897877 | 9904301 | a | 0 | ... | | chr10 | 3154988 | 3161009 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ___________ test_three_in_a_row[strandedness_chain86-method_chain86] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain115-method_chain115] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite'), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 5322411 | 5324403 | a | 0 | + | E | chr1 | 5453651 | 5458671 | a | 0 | + | E | chr1 | 3038992 | 3044396 | a | 0 | - | E | chr12 | 3105353 | 3105354 | a | 0 | + | E | chr14 | 1741463 | 1749349 | a | 0 | + | E | chr18 | 4973534 | 4975480 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 5322411 | 5326046 | a | 0 | - | E | chr1 | 3038992 | 3045878 | a | 0 | - | E | chr1 | 5048022 | 5048023 | a | 0 | - | E | chr12 | 1 | 2 | a | 0 | - | E | chr14 | 1741463 | 1742158 | a | 0 | - | E | chr18 | 6934271 | 6941097 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:104 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:106 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:12 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:14 E (and 40 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3ROrCthdM5KM2N0Zjy3n9G5ansUo7NF8C5G52L5agZGRwZHRiDB6MgIopmBXF4wFxmxAkW5GR1ZoCoRiAEoIQjU6KwXLwDWz+AcaLYaaIyz1KTpjI5Mzt6P78EUszgHmwejaHbWT/IEKnJinwWUdRKeAzTBSVQGqNtJ7hzYNAhicGI/geEkiO0gWagDwW4HmoaQB0KQ5AD6H+Qe58xz/6H+92W7BnM1k5PUKpBHmbaDPC31DORLPmMko5kgboJ7FKIL4lwoH2g5AI7PSvE=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain105-method_chain105] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 126 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain176-method_chain176] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain145-method_chain145] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite'), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain150-method_chain150] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 192 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ______________________ test_nearest[upstream-True-False] _______________________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 323, in test_nearest | @pytest.mark.parametrize("nearest_how,overlap,strandedness", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 3 distinct failures. (3 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 115, in _nearest | r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.Start, ocdf.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 62, in _next_nonoverlapping | r_idx, dist = nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_ends.values - 1, right_starts.values, right_indexes) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 34, in sorted_nearest.src.sorted_nearest.nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | (and 64 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGRyYGINuRkREswghDDAAx6wLX') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 351, in test_nearest | result = gr.nearest( | gr2, strandedness=strandedness, overlap=overlap, how=nearest_how) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 118, in _nearest | r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, | ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ocdf.End) | ^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | (and 69 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGRyYGINuRgREswghDDAAx2gLW') as a decorator on your test case +---------------- 3 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 359, in test_nearest | compare_results_nearest(bedtools_df, result) | ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 107, in compare_results_nearest | assert_df_equal(result_df, bedtools_df) | ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/helpers.py", line 60, in assert_df_equal | pd.testing.assert_frame_equal(df1, df2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 1279, in assert_frame_equal | assert_series_equal( | ~~~~~~~~~~~~~~~~~~~^ | lcol, | ^^^^^ | ...<12 lines>... | check_flags=False, | ^^^^^^^^^^^^^^^^^^ | ) | ^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 975, in assert_series_equal | assert_attr_equal("dtype", left, right, obj=f"Attributes of {obj}") | ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 421, in assert_attr_equal | raise_assert_detail(obj, msg, left_attr, right_attr) | ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pandas/_testing/asserters.py", line 614, in raise_assert_detail | raise AssertionError(msg) | AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different | | Attribute "dtype" are different | [left]: int32 | [right]: int64 | Falsifying example: test_nearest( | nearest_how='upstream', | overlap=True, | strandedness=False, | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/init.py:174 | (and 448 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjBIoxwPgAxwwLV') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfsjaqnoy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfsjaqnoy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx7euhzty/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx7euhzty/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2y6ylt3o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2y6ylt3o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyxxqqstv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyxxqqstv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjo6tfl7p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjo6tfl7p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfn_qqw4m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfn_qqw4m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzuaymayo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzuaymayo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyf9ehbp2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyf9ehbp2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcqh2ig7_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcqh2ig7_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj6zx0x9j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj6zx0x9j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa9_6guid/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa9_6guid/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7t8vhgi5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7t8vhgi5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkx4nlud_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkx4nlud_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptv7mjowl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptv7mjowl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4n3mvun9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4n3mvun9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_vqb43qh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_vqb43qh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcr_hfa4p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcr_hfa4p/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0lt1vjm1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0lt1vjm1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu0yd8wfy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu0yd8wfy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp78h3zo8e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp78h3zo8e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprkp8kt0v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprkp8kt0v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzuc0j6sh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzuc0j6sh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp80r8sqsk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp80r8sqsk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6gr4l5qs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6gr4l5qs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzeiqhsnw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzeiqhsnw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwui0vu7f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwui0vu7f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzb105w5m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzb105w5m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0kdrvauw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0kdrvauw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmfha4_tr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmfha4_tr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj106rj3j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj106rj3j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw1bhgd_d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw1bhgd_d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfjh3gko1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfjh3gko1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8som9tp_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8som9tp_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzhu3y_c8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzhu3y_c8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpycmbubdg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpycmbubdg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbu6l1gmv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbu6l1gmv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgtz3uxhw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgtz3uxhw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9n237wtk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9n237wtk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfwf4uyvg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfwf4uyvg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp30j_ltkc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp30j_ltkc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6vk8elao/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6vk8elao/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzjrvp7ba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzjrvp7ba/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphd124m0f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphd124m0f/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptbdozbd5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptbdozbd5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7_w__wal/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7_w__wal/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpim5ba_1s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpim5ba_1s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmzyozun_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmzyozun_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_iedsrh6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_iedsrh6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp359bhxjr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp359bhxjr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpybip8f6g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpybip8f6g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsi624wib/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsi624wib/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm5x7jttv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm5x7jttv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt4k4r8mw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt4k4r8mw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa3blr1vi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa3blr1vi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpadpvjtye/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpadpvjtye/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_60vemjg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_60vemjg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjzrd9l3f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjzrd9l3f/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu6l691f2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu6l691f2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph1img8k0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph1img8k0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxk5l51mx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxk5l51mx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjvsyqr_y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjvsyqr_y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqlt0rtpq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqlt0rtpq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplz5p0mnx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplz5p0mnx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwggpwivq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwggpwivq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpehtxu7cf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpehtxu7cf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp702_bq7m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp702_bq7m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpji284h7i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpji284h7i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzr_lvew6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzr_lvew6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqk2tvh05/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqk2tvh05/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpri3e40j6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpri3e40j6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0xelagpb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xelagpb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv5l9nslx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv5l9nslx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpva7g9q1i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpva7g9q1i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp32w82x95/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp32w82x95/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4bgj1sz3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4bgj1sz3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuisnf_2l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuisnf_2l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcv5i5hug/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcv5i5hug/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgg_wtzef/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgg_wtzef/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmxeeq63l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmxeeq63l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0_k9nepw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_k9nepw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1tx94vws/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1tx94vws/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl36e4ckw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl36e4ckw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpttgmxs59/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpttgmxs59/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe5zcd_lv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe5zcd_lv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9x67ao8j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9x67ao8j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9oevkwt6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9oevkwt6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0zbua80_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0zbua80_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6mbm_voj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6mbm_voj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxb1rjy4i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxb1rjy4i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz_jihj8f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz_jihj8f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5wjdspoq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5wjdspoq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpop_7jiv_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpop_7jiv_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjxvkx3rt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjxvkx3rt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp50v46z62/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp50v46z62/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyop8038b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyop8038b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy39e38vv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy39e38vv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmi9visjb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmi9visjb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc1tpd9pr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc1tpd9pr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfjlznjrd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfjlznjrd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzmn73utg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzmn73utg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3g533oa4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3g533oa4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7hz2kvbh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7hz2kvbh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2etdcge9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2etdcge9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6nui0jyn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6nui0jyn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4uiyiz26/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4uiyiz26/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnwl4v7b4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnwl4v7b4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpah2zqxo4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpah2zqxo4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7i7opufo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7i7opufo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8333xoud/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8333xoud/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy0efk4zi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy0efk4zi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8w8t2_hs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8w8t2_hs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf37v_4x4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf37v_4x4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr9d1759y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr9d1759y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzg02suov/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzg02suov/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_hbu7opa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_hbu7opa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaafm7fea/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaafm7fea/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjlxn476k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjlxn476k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppvsflezi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppvsflezi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6vai1he_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6vai1he_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeu93le2i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeu93le2i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2589taz3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2589taz3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2jxofblu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2jxofblu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvc99adpe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvc99adpe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0683kd20/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0683kd20/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkmwn126q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkmwn126q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcl0xo08c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcl0xo08c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5y234akq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5y234akq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplpkm27o7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplpkm27o7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsim1dax5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsim1dax5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdy0y1lmk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdy0y1lmk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppspqb764/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppspqb764/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph35ir4zk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph35ir4zk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptpso2_mx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptpso2_mx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpymagm79f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpymagm79f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp70mneby9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp70mneby9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_5uckeza/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_5uckeza/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdbsjf0wi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdbsjf0wi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpotl58k_o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpotl58k_o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpazj4bc6d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpazj4bc6d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf46gxxf9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf46gxxf9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp0knavoj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp0knavoj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprzvii7vr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprzvii7vr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpplzrut8d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpplzrut8d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprgqy7dhh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprgqy7dhh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp46rkyh3o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp46rkyh3o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6y4y4ojy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6y4y4ojy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6wz13y66/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6wz13y66/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe3pfsjc8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe3pfsjc8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz512_4qq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz512_4qq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb7z_vopo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb7z_vopo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiwc8gj95/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiwc8gj95/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz60ct01g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz60ct01g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe1z4zpgu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe1z4zpgu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2vqq61la/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2vqq61la/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxc5rh86_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxc5rh86_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpojl70h7p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpojl70h7p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2mn4b2w3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2mn4b2w3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4668wffz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4668wffz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1cjd0ysb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1cjd0ysb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuxs86ecz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuxs86ecz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnugkcesn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnugkcesn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe2en1jwz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe2en1jwz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm27dk098/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm27dk098/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp02oh2_q_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp02oh2_q_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo4efj73q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo4efj73q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 7337 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7337 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 7337 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 7337 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 7337 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 7337 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmgyzclle/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmgyzclle/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqjrwnlxi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqjrwnlxi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp18w2t8mi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp18w2t8mi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 7337 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7337 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 7337 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 7337 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 7337 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 7337 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphqv0ma0k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphqv0ma0k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprab_p9ww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprab_p9ww/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9yxqv_ji/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9yxqv_ji/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsltzxqkb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsltzxqkb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplnxlw3gr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplnxlw3gr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 7337 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7337 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 7337 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 7337 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 7337 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 7337 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgww2rkbn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgww2rkbn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpupaapqwn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpupaapqwn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp11oel50f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp11oel50f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_2y1p_ze/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_2y1p_ze/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_kfkjb9t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_kfkjb9t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8lj8ddwr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8lj8ddwr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphdtfw_m_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphdtfw_m_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmcmo2s5w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmcmo2s5w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptuv6bxma/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptuv6bxma/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7rhjdxyd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7rhjdxyd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp24r7zih5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp24r7zih5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyua2q_lm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyua2q_lm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl84mo44s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl84mo44s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl5z9evp9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl5z9evp9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiqr3o97z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiqr3o97z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwlvkt8gp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwlvkt8gp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn7_lvsds/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn7_lvsds/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo2v6ondu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo2v6ondu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0kruc6mz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0kruc6mz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphq1s4ru6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphq1s4ru6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2f2lcns4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2f2lcns4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw8st3yj4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw8st3yj4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4qgdort0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4qgdort0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmponbw6pa2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmponbw6pa2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx3_ntnxp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3_ntnxp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpavy6kyh3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpavy6kyh3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp80ysvuy8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp80ysvuy8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy85509gv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy85509gv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu5ixk2t0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu5ixk2t0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb91adekq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb91adekq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptybilnql/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptybilnql/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkjajctz8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkjajctz8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp92vq9cyp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp92vq9cyp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3v3ac4kz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3v3ac4kz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd0ywwx7d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd0ywwx7d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7sb77jun/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7sb77jun/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt4b72j5p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt4b72j5p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1ng9dhea/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ng9dhea/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpojae3s76/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpojae3s76/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiulz5zkx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiulz5zkx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4re54cgf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4re54cgf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcoigaj2c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcoigaj2c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpypu10a5v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpypu10a5v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgg7qahge/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgg7qahge/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3awlkb4m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3awlkb4m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdvwfxfke/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdvwfxfke/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe7gq9clm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7gq9clm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmporw0wcih/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmporw0wcih/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbhppkx6n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbhppkx6n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp597kjy_g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp597kjy_g/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpup73qx6s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpup73qx6s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpffvbt9rg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpffvbt9rg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpapxu9u5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpapxu9u5c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz8qq9uec/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz8qq9uec/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuz3l0o3y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuz3l0o3y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1q9du4va/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1q9du4va/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp01aegaur/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp01aegaur/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1ucekenz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ucekenz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7hdtir16/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7hdtir16/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmper85o1bt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmper85o1bt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptdplqu9l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptdplqu9l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd2ph8cvd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd2ph8cvd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4avseips/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4avseips/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptuttn62q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptuttn62q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp41u4vhgd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp41u4vhgd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpctbuc7qg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpctbuc7qg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4rtmd3gu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4rtmd3gu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_mldx7h6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_mldx7h6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_jkoq3eg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_jkoq3eg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2mbnt8ax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2mbnt8ax/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzywn8tue/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzywn8tue/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbfxxonkm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbfxxonkm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk9nmycu1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk9nmycu1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0snwj48r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0snwj48r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp4mha585/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp4mha585/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkdiqeiab/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkdiqeiab/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkug89azh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkug89azh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9xb2lx0i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9xb2lx0i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3gpyxw4e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3gpyxw4e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyb9eshqu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyb9eshqu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzbo7fm0y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzbo7fm0y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmped2d9tc7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmped2d9tc7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi1414noa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi1414noa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpizwfp8ro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpizwfp8ro/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp00oortzj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00oortzj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4ci4t108/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ci4t108/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy_j1c44l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy_j1c44l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppmrfxgyw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppmrfxgyw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu3r700l7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu3r700l7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjf7hy56a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjf7hy56a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6hp9fzjd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6hp9fzjd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqrf4o47b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqrf4o47b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpabiedka5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpabiedka5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1vw57cqa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1vw57cqa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoi0w3mbl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoi0w3mbl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk7yw3vdc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk7yw3vdc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_8vt3956/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_8vt3956/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq_c4f3ht/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq_c4f3ht/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj8pxax0q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj8pxax0q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3fudy5_y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3fudy5_y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj9ew2hbf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj9ew2hbf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkj9160ac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkj9160ac/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq_mpm5gj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq_mpm5gj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_52bswkw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_52bswkw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1plr63fr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1plr63fr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu03tkh8t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu03tkh8t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppeph0wuh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppeph0wuh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvettqqv_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvettqqv_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpisdaznb5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpisdaznb5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxfxvqnyq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxfxvqnyq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9wpvt2zx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9wpvt2zx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptdaxa4m4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptdaxa4m4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv20fujmf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv20fujmf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6b9ynpfx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6b9ynpfx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf4uqmhgh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf4uqmhgh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmploiguekn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmploiguekn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0d9sok3o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0d9sok3o/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9espwg9d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9espwg9d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy19lyei2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy19lyei2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq1g2178x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq1g2178x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuw_3npx0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuw_3npx0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2_f1gpvh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2_f1gpvh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo6fzh3p9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo6fzh3p9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_9qihlsf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_9qihlsf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd3rqu753/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd3rqu753/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpecx5xsov/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpecx5xsov/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfatx6zqu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfatx6zqu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppceo8b5v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppceo8b5v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpskos6r5x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpskos6r5x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxetbhgco/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxetbhgco/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1_unmnps/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1_unmnps/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaxbp3ft9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaxbp3ft9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb_v8nlvl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb_v8nlvl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxmgflrp0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxmgflrp0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _________________ test_k_nearest[upstream-False-opposite-last] _________________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 510, in test_k_nearest | @pytest.mark.explore | ^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 115, in nearest_previous | lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 28, in nearest_previous_idx | lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1s.values, d2e.values, d1s.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 28, in sorted_nearest.src.k_nearest.k_nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=False, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:14 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | (and 39 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBjRRRgBOKMDFg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py", line 548, in test_k_nearest | result = gr.k_nearest( | gr2, k=2, strandedness=strandedness, overlap=overlap, how=nearest_how, ties=ties) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2450, in k_nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 180, in _nearest | df = __nearest(d1, d2, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 140, in nearest_next | lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) | ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py", line 56, in nearest_next_idx | lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | d1e.values, d2s.values, d1e.index.values, ix, k, ties) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/k_nearest.pyx", line 55, in sorted_nearest.src.k_nearest.k_nearest_next_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_k_nearest( | nearest_how='upstream', | overlap=False, | strandedness='opposite', | ties='last', | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:160 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:171 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:41 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/k_nearest.py:42 | (and 41 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGMEijDDEAAAx1ALW') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx6w2z5b8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx6w2z5b8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp08fimh_4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp08fimh_4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp08n_4uwn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp08n_4uwn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5jr7eshe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5jr7eshe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa7gvhj03/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa7gvhj03/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_ciknlde/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ciknlde/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9w806qcg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9w806qcg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp50_zxh0c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp50_zxh0c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnpicoiik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnpicoiik/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzaj8ik_s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzaj8ik_s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi8gm9_0l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi8gm9_0l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvgpgtw82/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvgpgtw82/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0oz_nf03/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0oz_nf03/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1fn7ywij/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1fn7ywij/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdt3oe2ev/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdt3oe2ev/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4biosy14/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4biosy14/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt9ffuxx0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt9ffuxx0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7m4ir7bi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7m4ir7bi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfmett_rn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfmett_rn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkxspa3pf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkxspa3pf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt2t968zb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt2t968zb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj0lzh2xa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj0lzh2xa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmx0v7hey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmx0v7hey/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpksvokn7l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpksvokn7l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqeexij4h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqeexij4h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpir9hf6gd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpir9hf6gd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpusilzcn4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpusilzcn4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdbqp2sry/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdbqp2sry/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe1lgpfo3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe1lgpfo3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzzvtfdgt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzzvtfdgt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpus6cjlih/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpus6cjlih/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_gobm5wo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_gobm5wo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaw04oyo0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaw04oyo0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpje3tmva9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpje3tmva9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2bfe8vjm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2bfe8vjm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc1p6hook/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc1p6hook/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpazmo5i_z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpazmo5i_z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3bw0unec/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3bw0unec/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc5aob023/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc5aob023/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpabpf1dcn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpabpf1dcn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf5vwax6q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf5vwax6q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg89dapso/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg89dapso/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8wc2xpgv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8wc2xpgv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpixbvij2_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpixbvij2_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0xuijx7g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xuijx7g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbi2iyzem/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbi2iyzem/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd22t2t8f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd22t2t8f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeu2b67p0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeu2b67p0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxj6d0wi8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxj6d0wi8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbs0d2j68/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbs0d2j68/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuultijpm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuultijpm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdhme5m13/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdhme5m13/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdqdjy7uw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdqdjy7uw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuvel8h6x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuvel8h6x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp64rsanex/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp64rsanex/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8q_kcgbf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8q_kcgbf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsajkamc6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsajkamc6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxu8jgbum/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxu8jgbum/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp29cnee8y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp29cnee8y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpisodwnww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpisodwnww/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe_3r8jfs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe_3r8jfs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6pdzucm8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6pdzucm8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzaxzznjh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzaxzznjh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_i9ts0gl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_i9ts0gl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpthtbp_cj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpthtbp_cj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqhbzqo_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqhbzqo_h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplt8cthrx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplt8cthrx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjj8s37np/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjj8s37np/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnvbxk3l_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnvbxk3l_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4xkeaf94/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4xkeaf94/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdtafeup7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdtafeup7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1lw_910n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1lw_910n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9w5if0ep/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9w5if0ep/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxdy3ud86/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxdy3ud86/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdhdwoyqc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdhdwoyqc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjao_eh5p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjao_eh5p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvfqggx3a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvfqggx3a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpihd8r7pl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpihd8r7pl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3_vnz6l_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3_vnz6l_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7tq6br19/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7tq6br19/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7x6q99_y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7x6q99_y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjouz8b_1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjouz8b_1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpactb551n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpactb551n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplmcmxmby/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplmcmxmby/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpretx_4cp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpretx_4cp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbk_nkre1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbk_nkre1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy2q3ydyx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy2q3ydyx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqbfblgr0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqbfblgr0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiylubnmc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiylubnmc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy1xxbsih/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy1xxbsih/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzywmifkg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzywmifkg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_duzgzvf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_duzgzvf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx7w8b87e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx7w8b87e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn3b2e60j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn3b2e60j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptzql6eu0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptzql6eu0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpccih06a5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpccih06a5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqx09fat6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqx09fat6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfhc7y7eg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfhc7y7eg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0t17xdvm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0t17xdvm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnomih4zb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnomih4zb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjgxd0lhn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjgxd0lhn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeqqrpvn2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeqqrpvn2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprc5cno_r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprc5cno_r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp89ddsxl3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp89ddsxl3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpke99suj5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpke99suj5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp96qbdimg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp96qbdimg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp448emtff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp448emtff/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx_uwnrjo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx_uwnrjo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp300ji3sk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp300ji3sk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn9qgtwh6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn9qgtwh6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgqpjkmjc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgqpjkmjc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb5fvwfie/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb5fvwfie/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppvgfjcd5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppvgfjcd5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8aaafg6w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8aaafg6w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3pnccd9t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3pnccd9t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsqei66si/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsqei66si/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy44dcs8t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy44dcs8t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppvsyuoqh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppvsyuoqh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplh3vvmh1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplh3vvmh1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeobuy_pn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeobuy_pn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbmalai97/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbmalai97/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbpgeddu7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbpgeddu7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdapr5d9k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdapr5d9k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0jdyaxlh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0jdyaxlh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppt0vjqqu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppt0vjqqu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn72ohttc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn72ohttc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp258cxy0_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp258cxy0_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprty7idbt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprty7idbt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp45y70u_l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp45y70u_l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl3aeuqj4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl3aeuqj4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpejkp8r2e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpejkp8r2e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcc19u7w1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcc19u7w1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnut_bbzw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnut_bbzw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxd0wb3bq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxd0wb3bq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3b09j32x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3b09j32x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4gdaat7p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4gdaat7p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt5_spfef/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt5_spfef/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmdbor_5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmdbor_5a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaq_04nqr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaq_04nqr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3mg3zh_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3mg3zh_x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb888pdhm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb888pdhm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplj4isui0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplj4isui0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptgy356k8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptgy356k8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpejckepyj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpejckepyj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk5djit30/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk5djit30/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbrx4goa_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbrx4goa_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5woha_bj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5woha_bj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz74t68bd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz74t68bd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpifbvjqvm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpifbvjqvm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp60ts8i8g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp60ts8i8g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphjd40q08/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphjd40q08/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwwk1vgta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwwk1vgta/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp138airuo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp138airuo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwd0n1nbv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwd0n1nbv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpza8rvld9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpza8rvld9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0g1m7g1k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0g1m7g1k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpadrwa2ry/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpadrwa2ry/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxuq0y9wl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxuq0y9wl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplgi_s963/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplgi_s963/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3js60zmg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3js60zmg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp93h76xj_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp93h76xj_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp879m1inb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp879m1inb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0fqf_ad7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0fqf_ad7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9kf6g4yv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9kf6g4yv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2ja27uce/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ja27uce/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpew9eof0m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpew9eof0m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3zlvjzra/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3zlvjzra/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgkbi8fxh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgkbi8fxh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfo43re1m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfo43re1m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpltjive7z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpltjive7z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk500pgwk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk500pgwk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq9wckkmf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9wckkmf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp34ol29au/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp34ol29au/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpms7a_22_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpms7a_22_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4m1xvpsi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4m1xvpsi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpij69_ql1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpij69_ql1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp221uj_kb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp221uj_kb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuw_85r6h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuw_85r6h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm9flalwy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm9flalwy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplt3gsz15/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplt3gsz15/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvg3q8iiu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvg3q8iiu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsibe8nt7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsibe8nt7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpavuj82ae/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpavuj82ae/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. __________ test_three_in_a_row[strandedness_chain125-method_chain125] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite'), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') __________ test_three_in_a_row[strandedness_chain187-method_chain187] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6357289 | 6357290 | a | 0 | + | | chr7 | 149592 | 149593 | a | 0 | + | | chr12 | 6048085 | 6048086 | a | 0 | + | | chr19 | 1527408 | 1527409 | a | 0 | + | | chrM | 3988944 | 3988945 | a | 0 | + | | chrY | 10000000 | 10000001 | a | 0 | + | | chrY | 6048085 | 6048086 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain151-method_chain151] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ___________ test_three_in_a_row[strandedness_chain87-method_chain87] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOGwJCBESHFBBEHAF5KBB8=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') __________ test_three_in_a_row[strandedness_chain106-method_chain106] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 101 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain180-method_chain180] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 109 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain117-method_chain117] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain147-method_chain147] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 260 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain166-method_chain166] __________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:373 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ___________ test_three_in_a_row[strandedness_chain75-method_chain75] ___________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 9955182 | 9955183 | a | 0 | + | | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 | (and 27 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZHQWkY9kYHAEQkZHBheG6c/zGBwZwQgowAiRgYsASTBkAADqtgde') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'same'), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain188-method_chain188] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain126-method_chain126] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/attr.py:65 E (and 180 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain107-method_chain107] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ___________ test_three_in_a_row[strandedness_chain88-method_chain88] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain152-method_chain152] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/init.py:174 E (and 202 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain127-method_chain127] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain148-method_chain148] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/init.py:174 E (and 201 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain182-method_chain182] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 130 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain209-method_chain209] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ___________ test_three_in_a_row[strandedness_chain89-method_chain89] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr7 | 1 | 2 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr12 | 1 | 2 | a | 0 | + | | chr14 | 1 | 2 | a | 0 | + | | chr16 | 1 | 2 | a | 0 | + | | chr20 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3057563 | 3059989 | a | 0 | + | | chr1 | 9923147 | 9932338 | a | 0 | + | | chr1 | 7344815 | 7354814 | a | 0 | + | | chr1 | 5154736 | 5156458 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 7344815 | 7348111 | a | 0 | + | | chr1 | 9207601 | 9212374 | a | 0 | + | | chr1 | 7344815 | 7347765 | a | 0 | + | | chr1 | 2214319 | 2216913 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr12 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr12 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr12 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr4 | 1 | 2 | a | 0 | + | | chr4 | 1 | 2 | a | 0 | + | | chr4 | 1 | 2 | a | 0 | + | | chr12 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr12 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6 | 7 | a | 0 | + | | chr1 | 6 | 7 | a | 0 | + | | chr1 | 6 | 7 | a | 0 | + | | chr12 | 6 | 7 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr12 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6766191 | 6766192 | a | 0 | - | | chr1 | 6766191 | 6766192 | a | 0 | - | | chr1 | 6766191 | 6766192 | a | 0 | - | | chr12 | 6766191 | 6766192 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr12 | 6766191 | 6766192 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr12 | 6766191 | 6766192 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr12 | 6766191 | 6766192 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr12 | 6766191 | 6766192 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr12 | 6766191 | 6766192 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr12 | 6766191 | 6766192 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr12 | 6766191 | 6766192 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr12 | 6766191 | 6766192 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6766191 | 6766192 | a | 0 | - | | chr1 | 6766191 | 6766192 | a | 0 | - | | chr1 | 6766191 | 6766192 | a | 0 | - | | chr12 | 6766191 | 6766192 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr1 | 6766191 | 6766192 | a | 0 | + | | chr12 | 6766191 | 6766192 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr12 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr12 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr12 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr12 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr12 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr12 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr12 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr12 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr12 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr12 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | | chr12 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr4 | 1 | 2 | a | 0 | + | | chr4 | 1 | 2 | a | 0 | + | | chr4 | 1 | 2 | a | 0 | + | | chr4 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ___________ test_three_in_a_row[strandedness_chain76-method_chain76] ___________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') __________ test_three_in_a_row[strandedness_chain153-method_chain153] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 195 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') _____________________________ test_coverage[False] _____________________________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", strandedness) tests/test_binary.py:207: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:238: in test_coverage result = gr.coverage(gr2, strandedness=strandedness) pyranges/pyranges.py:1341: in coverage other = other.merge(count=True, strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_coverage( E strandedness=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3SWOLOPgcGREYYYGIEkMh8AXJoEOA==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpztjh1sme/f1.bed -b /tmp/tmpztjh1sme/f2.bed Chromosome Start End Name Score Strand 0 chr3 7853242 7859915 a 0 + Chromosome Start End Name Score Strand 0 chr8 261124 265272 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpe_wug714/f1.bed -b /tmp/tmpe_wug714/f2.bed Chromosome Start End Name Score Strand 0 chr8 261124 265272 a 0 - Chromosome Start End Name Score Strand 0 chr8 261124 265272 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpw66e9lp_/f1.bed -b /tmp/tmpw66e9lp_/f2.bed Chromosome Start End Name Score Strand 0 chr8 4148 8296 a 0 - Chromosome Start End Name Score Strand 0 chr8 261124 265272 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpa7s11x5k/f1.bed -b /tmp/tmpa7s11x5k/f2.bed Chromosome Start End Name Score Strand 0 chr8 4148 8296 a 0 - Chromosome Start End Name Score Strand 0 chr8 1 4149 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmplhxkg7wg/f1.bed -b /tmp/tmplhxkg7wg/f2.bed Chromosome Start End Name Score Strand 0 chr8 4148 8296 a 0 + Chromosome Start End Name Score Strand 0 chr8 1 4149 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp82z524bn/f1.bed -b /tmp/tmp82z524bn/f2.bed Chromosome Start End Name Score Strand 0 chr8 4148 4149 a 0 + Chromosome Start End Name Score Strand 0 chr8 1 4149 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmps7npv5xa/f1.bed -b /tmp/tmps7npv5xa/f2.bed Chromosome Start End Name Score Strand 0 chr8 4148 4149 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 4149 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpzqxozhwf/f1.bed -b /tmp/tmpzqxozhwf/f2.bed Chromosome Start End Name Score Strand 0 chr1 2 7917 a 0 + 1 chr1 5652686 5662288 a 0 + 2 chr1 5610192 5611316 a 0 + 3 chr1 9151373 9159894 a 0 + 4 chr1 6210430 6213225 a 0 - 5 chr1 378349 384817 a 0 - 6 chr1 2470425 2470426 a 0 - 7 chr1 7064158 7073529 a 0 - 8 chr19 7834751 7842763 a 0 + Chromosome Start End Name Score Strand 0 chr1 2803441 2805754 a 0 + 1 chr1 5003317 5005355 a 0 + 2 chr1 9818514 9823799 a 0 - 3 chr1 7752470 7762138 a 0 - 4 chr10 3423254 3430945 a 0 - 5 chr13 777145 786146 a 0 - 6 chr15 9707000 9713737 a 0 + 7 chr16 545527 547622 a 0 - 8 chr19 2942134 2949868 a 0 + 9 chr19 2384083 2389092 a 0 - 10 chr19 6080052 6080054 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpptjox_cf/f1.bed -b /tmp/tmpptjox_cf/f2.bed Chromosome Start End Name Score Strand 0 chr1 2 7917 a 0 + 1 chr1 5652686 5662288 a 0 + 2 chr1 5610192 5611316 a 0 + 3 chr1 9151373 9159894 a 0 + 4 chr1 6210430 6213225 a 0 - 5 chr1 378349 384817 a 0 - 6 chr1 2470425 2470426 a 0 - 7 chr1 7064158 7073529 a 0 - 8 chr19 7834751 7842763 a 0 + Chromosome Start End Name Score Strand 0 chr1 2803441 2805754 a 0 + 1 chr1 5003317 5005355 a 0 + 2 chr1 9818514 9823799 a 0 - 3 chr1 7752470 7762138 a 0 - 4 chr10 3423254 3430945 a 0 - 5 chr13 777145 786146 a 0 - 6 chr15 9707000 9713737 a 0 + 7 chr16 545527 547622 a 0 - 8 chr19 2942134 2949868 a 0 + 9 chr19 2384083 2389092 a 0 - 10 chr19 6080052 6080054 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpt8udto11/f1.bed -b /tmp/tmpt8udto11/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp8oacrb72/f1.bed -b /tmp/tmp8oacrb72/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpm93yico9/f1.bed -b /tmp/tmpm93yico9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpk17c0t6s/f1.bed -b /tmp/tmpk17c0t6s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpkzkhlpye/f1.bed -b /tmp/tmpkzkhlpye/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2 5168 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp3v2dz6hd/f1.bed -b /tmp/tmp3v2dz6hd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp8an6ipth/f1.bed -b /tmp/tmp8an6ipth/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8260395 8262218 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfd9x80rl/f1.bed -b /tmp/tmpfd9x80rl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpc0zowpmy/f1.bed -b /tmp/tmpc0zowpmy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6144 10393 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp8senqzd8/f1.bed -b /tmp/tmp8senqzd8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpxqmfeyf4/f1.bed -b /tmp/tmpxqmfeyf4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4425475 4427678 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_ul0dmz4/f1.bed -b /tmp/tmp_ul0dmz4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp8hmd6_4w/f1.bed -b /tmp/tmp8hmd6_4w/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr17 4037736 4038027 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp6wod04u8/f1.bed -b /tmp/tmp6wod04u8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1vijkwsw/f1.bed -b /tmp/tmp1vijkwsw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9271707 9279339 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpx6b8i8he/f1.bed -b /tmp/tmpx6b8i8he/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpwfgksdde/f1.bed -b /tmp/tmpwfgksdde/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4319870 4324468 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmppmref_q1/f1.bed -b /tmp/tmppmref_q1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmppt6fs4r4/f1.bed -b /tmp/tmppt6fs4r4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3239534 3247173 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpyxn7vrcf/f1.bed -b /tmp/tmpyxn7vrcf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpofj10q66/f1.bed -b /tmp/tmpofj10q66/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1411820 1411864 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp51nt71ms/f1.bed -b /tmp/tmp51nt71ms/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpgdq3ox3f/f1.bed -b /tmp/tmpgdq3ox3f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr8 753743 758322 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp71qmo_gp/f1.bed -b /tmp/tmp71qmo_gp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfrzzntjk/f1.bed -b /tmp/tmpfrzzntjk/f2.bed Chromosome Start End Name Score Strand 0 chr1 3240 3241 a 0 - 1 chr1 3240 3241 a 0 - Chromosome Start End Name Score Strand 0 chr1 5963525 5966739 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpxbq8efqy/f1.bed -b /tmp/tmpxbq8efqy/f2.bed Chromosome Start End Name Score Strand 0 chr1 3240 3241 a 0 - 1 chr1 3240 3241 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpm2x_4_gb/f1.bed -b /tmp/tmpm2x_4_gb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4194763 4194986 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpenhjngbx/f1.bed -b /tmp/tmpenhjngbx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmprp337dcb/f1.bed -b /tmp/tmprp337dcb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5070170 5078287 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpyz95k4o7/f1.bed -b /tmp/tmpyz95k4o7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpj71w6fkd/f1.bed -b /tmp/tmpj71w6fkd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 3034533 3042700 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmplylgy3zr/f1.bed -b /tmp/tmplylgy3zr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_f702ebv/f1.bed -b /tmp/tmp_f702ebv/f2.bed Chromosome Start End Name Score Strand 0 chr1 3400 3401 a 0 + 1 chr1 3400 3401 a 0 - Chromosome Start End Name Score Strand 0 chr1 3871278 3872296 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpc1jwegjd/f1.bed -b /tmp/tmpc1jwegjd/f2.bed Chromosome Start End Name Score Strand 0 chr1 3400 3401 a 0 + 1 chr1 3400 3401 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpjgldrcwk/f1.bed -b /tmp/tmpjgldrcwk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2422629 2427069 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpyg64ler3/f1.bed -b /tmp/tmpyg64ler3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpba7bst52/f1.bed -b /tmp/tmpba7bst52/f2.bed Chromosome Start End Name Score Strand 0 chr1 9953 9954 a 0 + 1 chr1 9953 9954 a 0 - Chromosome Start End Name Score Strand 0 chr1 2604110 2607819 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpyzktufw7/f1.bed -b /tmp/tmpyzktufw7/f2.bed Chromosome Start End Name Score Strand 0 chr1 9953 9954 a 0 + 1 chr1 9953 9954 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1oancc3x/f1.bed -b /tmp/tmp1oancc3x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3710101 3711708 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp28a_w22y/f1.bed -b /tmp/tmp28a_w22y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmplkry_erb/f1.bed -b /tmp/tmplkry_erb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3284632 3288053 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp974te2a6/f1.bed -b /tmp/tmp974te2a6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_kfkkzwi/f1.bed -b /tmp/tmp_kfkkzwi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2054802 2056933 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpti3k9sz0/f1.bed -b /tmp/tmpti3k9sz0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpp59_xvfj/f1.bed -b /tmp/tmpp59_xvfj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr17 3004137 3011890 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpkna9g91_/f1.bed -b /tmp/tmpkna9g91_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpjylcbzrt/f1.bed -b /tmp/tmpjylcbzrt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6999873 7008518 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp3ohuwdnk/f1.bed -b /tmp/tmp3ohuwdnk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp4uzz5_rl/f1.bed -b /tmp/tmp4uzz5_rl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6294195 6297645 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpp317c2tx/f1.bed -b /tmp/tmpp317c2tx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp70x1mqac/f1.bed -b /tmp/tmp70x1mqac/f2.bed Chromosome Start End Name Score Strand 0 chr1 5673 5674 a 0 - 1 chr1 5673 5674 a 0 - Chromosome Start End Name Score Strand 0 chr1 8696356 8702845 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpd7pkxpcd/f1.bed -b /tmp/tmpd7pkxpcd/f2.bed Chromosome Start End Name Score Strand 0 chr1 5673 5674 a 0 - 1 chr1 5673 5674 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpeaykn6c3/f1.bed -b /tmp/tmpeaykn6c3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9061884 9070516 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp3bbrencg/f1.bed -b /tmp/tmp3bbrencg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpad8soeog/f1.bed -b /tmp/tmpad8soeog/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpztvuefkt/f1.bed -b /tmp/tmpztvuefkt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmptmathiw2/f1.bed -b /tmp/tmptmathiw2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9337413 9338823 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp0s4ga2pf/f1.bed -b /tmp/tmp0s4ga2pf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp0rxjd8l6/f1.bed -b /tmp/tmp0rxjd8l6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 245263 247923 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpr4apgecl/f1.bed -b /tmp/tmpr4apgecl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpe29zbi58/f1.bed -b /tmp/tmpe29zbi58/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7007665 7007669 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmprzc9e523/f1.bed -b /tmp/tmprzc9e523/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpp9hihvxt/f1.bed -b /tmp/tmpp9hihvxt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1431057 1435053 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp5uj2r0v2/f1.bed -b /tmp/tmp5uj2r0v2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpbjusue33/f1.bed -b /tmp/tmpbjusue33/f2.bed Chromosome Start End Name Score Strand 0 chr1 4759 4760 a 0 + 1 chr1 4759 4760 a 0 - Chromosome Start End Name Score Strand 0 chr1 9096995 9102147 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpgznhc81i/f1.bed -b /tmp/tmpgznhc81i/f2.bed Chromosome Start End Name Score Strand 0 chr1 4759 4760 a 0 + 1 chr1 4759 4760 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpv7qg3sjq/f1.bed -b /tmp/tmpv7qg3sjq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9577267 9584565 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpx2t8fadr/f1.bed -b /tmp/tmpx2t8fadr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpg8mwn1b9/f1.bed -b /tmp/tmpg8mwn1b9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4859526 4862737 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpg14ydpzn/f1.bed -b /tmp/tmpg14ydpzn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmppd9zrlxx/f1.bed -b /tmp/tmppd9zrlxx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4605402 4607843 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpsw2ik91m/f1.bed -b /tmp/tmpsw2ik91m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpwzf2swd8/f1.bed -b /tmp/tmpwzf2swd8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr7 5323344 5324801 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpz2vc80xi/f1.bed -b /tmp/tmpz2vc80xi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpik9mtmrd/f1.bed -b /tmp/tmpik9mtmrd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7506807 7510126 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpny9e3e5m/f1.bed -b /tmp/tmpny9e3e5m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmptmisr39z/f1.bed -b /tmp/tmptmisr39z/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3380815 3381622 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpy16h2ivp/f1.bed -b /tmp/tmpy16h2ivp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp9w3_h7tf/f1.bed -b /tmp/tmp9w3_h7tf/f2.bed Chromosome Start End Name Score Strand 0 chr1 3511 3512 a 0 - 1 chr1 3511 3512 a 0 - Chromosome Start End Name Score Strand 0 chr1 7621276 7630391 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp4kvx5x7y/f1.bed -b /tmp/tmp4kvx5x7y/f2.bed Chromosome Start End Name Score Strand 0 chr1 3511 3512 a 0 - 1 chr1 3511 3512 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpg3vhafqh/f1.bed -b /tmp/tmpg3vhafqh/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 541894 549654 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpul36v5ma/f1.bed -b /tmp/tmpul36v5ma/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpwvs6ud55/f1.bed -b /tmp/tmpwvs6ud55/f2.bed Chromosome Start End Name Score Strand 0 chr1 3692 3693 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 4352 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpyemts3kq/f1.bed -b /tmp/tmpyemts3kq/f2.bed Chromosome Start End Name Score Strand 0 chr1 3692 3693 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpufkwgyjc/f1.bed -b /tmp/tmpufkwgyjc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7202237 7204839 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmprpqrpe2n/f1.bed -b /tmp/tmprpqrpe2n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpjvd_ys_t/f1.bed -b /tmp/tmpjvd_ys_t/f2.bed Chromosome Start End Name Score Strand 0 chr3 1 2 a 0 - 1 chr3 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9499919 9507484 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpf5pjsybr/f1.bed -b /tmp/tmpf5pjsybr/f2.bed Chromosome Start End Name Score Strand 0 chr3 1 2 a 0 - 1 chr3 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp64nj0ych/f1.bed -b /tmp/tmp64nj0ych/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6016232 6020568 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpwmo9f2xm/f1.bed -b /tmp/tmpwmo9f2xm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_ui_3h21/f1.bed -b /tmp/tmp_ui_3h21/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 10000000 10000597 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpamy46eyf/f1.bed -b /tmp/tmpamy46eyf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpaafir8ga/f1.bed -b /tmp/tmpaafir8ga/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2751017 2757397 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmptc9220cy/f1.bed -b /tmp/tmptc9220cy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp3hatah8x/f1.bed -b /tmp/tmp3hatah8x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3778144 3788144 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpyqsn8ow3/f1.bed -b /tmp/tmpyqsn8ow3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpipp_6w8g/f1.bed -b /tmp/tmpipp_6w8g/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3660800 3661235 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp4m_snfk1/f1.bed -b /tmp/tmp4m_snfk1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp3lc51siv/f1.bed -b /tmp/tmp3lc51siv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7356623 7361370 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmphr2okkx3/f1.bed -b /tmp/tmphr2okkx3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmprq5vd5w1/f1.bed -b /tmp/tmprq5vd5w1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5572212 5577031 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpgq2tnou_/f1.bed -b /tmp/tmpgq2tnou_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp92urexlv/f1.bed -b /tmp/tmp92urexlv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2747832 2754933 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpzfqyy888/f1.bed -b /tmp/tmpzfqyy888/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpo9ji_ybo/f1.bed -b /tmp/tmpo9ji_ybo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 1285 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpiab3uk_d/f1.bed -b /tmp/tmpiab3uk_d/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpku9m_f9i/f1.bed -b /tmp/tmpku9m_f9i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2598406 2602432 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpd4rjw3g3/f1.bed -b /tmp/tmpd4rjw3g3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpk5wh091n/f1.bed -b /tmp/tmpk5wh091n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chrM 5118776 5123019 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmplrk3u98x/f1.bed -b /tmp/tmplrk3u98x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpcv7ttu72/f1.bed -b /tmp/tmpcv7ttu72/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2968740 2977496 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpmu73lvmk/f1.bed -b /tmp/tmpmu73lvmk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpdfl_ggvt/f1.bed -b /tmp/tmpdfl_ggvt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9745853 9746960 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmps_hjspis/f1.bed -b /tmp/tmps_hjspis/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpym08eotz/f1.bed -b /tmp/tmpym08eotz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpnod4b43f/f1.bed -b /tmp/tmpnod4b43f/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp56ek01sp/f1.bed -b /tmp/tmp56ek01sp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr15 1343247 1348151 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp19hshyyg/f1.bed -b /tmp/tmp19hshyyg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpm74ati3i/f1.bed -b /tmp/tmpm74ati3i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1475410 1475411 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpnr773mss/f1.bed -b /tmp/tmpnr773mss/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp9xta59k3/f1.bed -b /tmp/tmp9xta59k3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3617547 3619953 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpi87bvddi/f1.bed -b /tmp/tmpi87bvddi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpa8wdw02x/f1.bed -b /tmp/tmpa8wdw02x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6220349 6226320 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpwa6dr1np/f1.bed -b /tmp/tmpwa6dr1np/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpteav4op9/f1.bed -b /tmp/tmpteav4op9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 685690 691216 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpza5ofa7k/f1.bed -b /tmp/tmpza5ofa7k/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5934358 5936832 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp92u_4ssi/f1.bed -b /tmp/tmp92u_4ssi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfcvuq2au/f1.bed -b /tmp/tmpfcvuq2au/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr9 8004642 8014057 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmptpahtqon/f1.bed -b /tmp/tmptpahtqon/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmps9aayh8r/f1.bed -b /tmp/tmps9aayh8r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6775166 6775888 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpnp9qi5f1/f1.bed -b /tmp/tmpnp9qi5f1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmptlk_89x0/f1.bed -b /tmp/tmptlk_89x0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9359723 9365419 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_fqbfewl/f1.bed -b /tmp/tmp_fqbfewl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpecv9vj2o/f1.bed -b /tmp/tmpecv9vj2o/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 - 1 chr2 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 2060263 2065772 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpbo89uz0x/f1.bed -b /tmp/tmpbo89uz0x/f2.bed Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 - 1 chr2 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp08nktd43/f1.bed -b /tmp/tmp08nktd43/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5951207 5952136 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpy6h84kyx/f1.bed -b /tmp/tmpy6h84kyx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp73taqze8/f1.bed -b /tmp/tmp73taqze8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4302850 4312089 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqvni58dm/f1.bed -b /tmp/tmpqvni58dm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpi_r737o8/f1.bed -b /tmp/tmpi_r737o8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3205397 3205398 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpaytrfnj2/f1.bed -b /tmp/tmpaytrfnj2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpvf_u3vvb/f1.bed -b /tmp/tmpvf_u3vvb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr9 6346543 6350198 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp75wzse7a/f1.bed -b /tmp/tmp75wzse7a/f2.bed Chromosome Start End Name Score Strand 0 chr1 1879 1880 a 0 - 1 chr1 1879 1880 a 0 - Chromosome Start End Name Score Strand 0 chr1 6420477 6428066 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpgorpmo_d/f1.bed -b /tmp/tmpgorpmo_d/f2.bed Chromosome Start End Name Score Strand 0 chr1 1879 1880 a 0 - 1 chr1 1879 1880 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpr_hj134h/f1.bed -b /tmp/tmpr_hj134h/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7666676 7676128 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmptyltg8mx/f1.bed -b /tmp/tmptyltg8mx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpralmlwad/f1.bed -b /tmp/tmpralmlwad/f2.bed Chromosome Start End Name Score Strand 0 chr1 1023 1024 a 0 + 1 chr1 1023 1024 a 0 - Chromosome Start End Name Score Strand 0 chr1 1459566 1462530 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1x3ew3cb/f1.bed -b /tmp/tmp1x3ew3cb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1023 1024 a 0 + 1 chr1 1023 1024 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpq806bsnj/f1.bed -b /tmp/tmpq806bsnj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr22 9803101 9812188 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp73mtjpbm/f1.bed -b /tmp/tmp73mtjpbm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfrok2dvj/f1.bed -b /tmp/tmpfrok2dvj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1410506 1415372 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpyhb9rnfj/f1.bed -b /tmp/tmpyhb9rnfj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpvv68vz45/f1.bed -b /tmp/tmpvv68vz45/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3240387 3247771 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpaemkm032/f1.bed -b /tmp/tmpaemkm032/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpwkfscavw/f1.bed -b /tmp/tmpwkfscavw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6843697 6851030 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpziml21qp/f1.bed -b /tmp/tmpziml21qp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpl51j68d2/f1.bed -b /tmp/tmpl51j68d2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 6094634 6097955 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpa5l0o88s/f1.bed -b /tmp/tmpa5l0o88s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp035g3rjs/f1.bed -b /tmp/tmp035g3rjs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5250614 5254068 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpjxw4sjbb/f1.bed -b /tmp/tmpjxw4sjbb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmptgvmrapj/f1.bed -b /tmp/tmptgvmrapj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 734168 739553 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmph78c3wxi/f1.bed -b /tmp/tmph78c3wxi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmplcexqmy1/f1.bed -b /tmp/tmplcexqmy1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 668551 671994 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpf14e73xp/f1.bed -b /tmp/tmpf14e73xp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpw631rwri/f1.bed -b /tmp/tmpw631rwri/f2.bed Chromosome Start End Name Score Strand 0 chr1 8392 8393 a 0 - 1 chr1 8392 8393 a 0 - Chromosome Start End Name Score Strand 0 chr1 4826577 4831468 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpag1z68st/f1.bed -b /tmp/tmpag1z68st/f2.bed Chromosome Start End Name Score Strand 0 chr1 8392 8393 a 0 - 1 chr1 8392 8393 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpjj7p70oo/f1.bed -b /tmp/tmpjj7p70oo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chrX 9561222 9562271 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpxvvpmtvq/f1.bed -b /tmp/tmpxvvpmtvq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpx2b1wf3s/f1.bed -b /tmp/tmpx2b1wf3s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8407122 8409861 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpw8vveb7d/f1.bed -b /tmp/tmpw8vveb7d/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp4n4qrw8w/f1.bed -b /tmp/tmp4n4qrw8w/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 9301120 9302398 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpcwumqlqm/f1.bed -b /tmp/tmpcwumqlqm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpnjj1ty9x/f1.bed -b /tmp/tmpnjj1ty9x/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr22 3288110 3288605 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpohi4moyf/f1.bed -b /tmp/tmpohi4moyf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpk4pmfjsy/f1.bed -b /tmp/tmpk4pmfjsy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp97elyaq4/f1.bed -b /tmp/tmp97elyaq4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmprhbf207j/f1.bed -b /tmp/tmprhbf207j/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 3435872 3437415 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmps8qgx1l5/f1.bed -b /tmp/tmps8qgx1l5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1871349 1871501 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpnvzmj0vx/f1.bed -b /tmp/tmpnvzmj0vx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp2982bow8/f1.bed -b /tmp/tmp2982bow8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 5956540 5961567 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpzrleixp7/f1.bed -b /tmp/tmpzrleixp7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpi9s7hk68/f1.bed -b /tmp/tmpi9s7hk68/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 8178839 8188149 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_smu8iq8/f1.bed -b /tmp/tmp_smu8iq8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfc_5eqsk/f1.bed -b /tmp/tmpfc_5eqsk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7506453 7514037 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpc6joh7fm/f1.bed -b /tmp/tmpc6joh7fm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpvbccs8sa/f1.bed -b /tmp/tmpvbccs8sa/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr17 1096424 1098368 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpjr_90lv0/f1.bed -b /tmp/tmpjr_90lv0/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 7224368 7225796 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpnhupz336/f1.bed -b /tmp/tmpnhupz336/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpms19yxcw/f1.bed -b /tmp/tmpms19yxcw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr10 8305168 8311003 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmprjb8dope/f1.bed -b /tmp/tmprjb8dope/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfbquxrpv/f1.bed -b /tmp/tmpfbquxrpv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpaqmg5lki/f1.bed -b /tmp/tmpaqmg5lki/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp7d8gqw3y/f1.bed -b /tmp/tmp7d8gqw3y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1048417 1058417 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1lyxtkkq/f1.bed -b /tmp/tmp1lyxtkkq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpbfkr1x5b/f1.bed -b /tmp/tmpbfkr1x5b/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1878326 1878935 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpywucdi5d/f1.bed -b /tmp/tmpywucdi5d/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp28gs1sbp/f1.bed -b /tmp/tmp28gs1sbp/f2.bed Chromosome Start End Name Score Strand 0 chr1 8013 8014 a 0 - 1 chr1 8013 8014 a 0 - Chromosome Start End Name Score Strand 0 chr1 6509316 6509317 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpl3x6nsws/f1.bed -b /tmp/tmpl3x6nsws/f2.bed Chromosome Start End Name Score Strand 0 chr1 8013 8014 a 0 - 1 chr1 8013 8014 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpzn7o3eji/f1.bed -b /tmp/tmpzn7o3eji/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 4288662 4296027 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpn47vu8rm/f1.bed -b /tmp/tmpn47vu8rm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 - 1 chr1 1 2 a 0 - Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp4cqz1ao1/f1.bed -b /tmp/tmp4cqz1ao1/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1200060 1202981 a 0 + 1 chr1 8266367 8272802 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp82il81vc/f1.bed -b /tmp/tmp82il81vc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3805979 3812181 a 0 - 1 chr10 7848893 7852424 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpztwb0wr3/f1.bed -b /tmp/tmpztwb0wr3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 24447 34335 a 0 + 1 chr1 353166 356759 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmps_vcsgbs/f1.bed -b /tmp/tmps_vcsgbs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2956 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqohe5vzk/f1.bed -b /tmp/tmpqohe5vzk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2471056 2480807 a 0 - 1 chr1 9958105 9959354 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpcotsw9fr/f1.bed -b /tmp/tmpcotsw9fr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 6451 a 0 - 1 chr1 1 6451 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpyct2j08u/f1.bed -b /tmp/tmpyct2j08u/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8612382 8612705 a 0 + 1 chr1 7178519 7185417 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmprd35iq__/f1.bed -b /tmp/tmprd35iq__/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7391754 7397750 a 0 + 1 chr14 9999999 10001925 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp5yfn3vt5/f1.bed -b /tmp/tmp5yfn3vt5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9764914 9772495 a 0 - 1 chr9 3934666 3937963 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpjrv67uku/f1.bed -b /tmp/tmpjrv67uku/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2644662 2648683 a 0 - 1 chr7 1 4580 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmplhgsmyio/f1.bed -b /tmp/tmplhgsmyio/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4824208 4833527 a 0 - 1 chr6 5248350 5251428 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpttpfzyli/f1.bed -b /tmp/tmpttpfzyli/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9717181 9717183 a 0 + 1 chr1 5640739 5647158 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmphbvc4665/f1.bed -b /tmp/tmphbvc4665/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 410180 411756 a 0 + 1 chr1 410180 417690 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpa4vqcrly/f1.bed -b /tmp/tmpa4vqcrly/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 297631 303714 a 0 - 1 chr1 6416367 6417302 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmphk2fw1yy/f1.bed -b /tmp/tmphk2fw1yy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6019260 6019261 a 0 + 1 chr1 251181 256433 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpyv1gwhfx/f1.bed -b /tmp/tmpyv1gwhfx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9373 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpv1tg84iv/f1.bed -b /tmp/tmpv1tg84iv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 9999999 10009741 a 0 - 1 chr20 3605540 3611708 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpr39gj9gw/f1.bed -b /tmp/tmpr39gj9gw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7278720 7279830 a 0 - 1 chr21 1244502 1250553 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp23y6xbyl/f1.bed -b /tmp/tmp23y6xbyl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 202338 204396 a 0 - 1 chr10 9117671 9122207 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpc1vtbs2e/f1.bed -b /tmp/tmpc1vtbs2e/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 500 a 0 + 1 chr1 1 5708 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfgq_lvv4/f1.bed -b /tmp/tmpfgq_lvv4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4449166 4449570 a 0 - 1 chr1 636552 639247 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpp3__o05j/f1.bed -b /tmp/tmpp3__o05j/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9961981 9966464 a 0 + 1 chr1 3277009 3284228 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpxtc_x30p/f1.bed -b /tmp/tmpxtc_x30p/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6707062 6709034 a 0 - 1 chr5 628130 628282 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp2clzjy6s/f1.bed -b /tmp/tmp2clzjy6s/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8722237 8725756 a 0 - 1 chr16 509294 514067 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpco7uclv8/f1.bed -b /tmp/tmpco7uclv8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2790626 2795719 a 0 - 1 chr9 10000000 10005481 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp9i385rsg/f1.bed -b /tmp/tmp9i385rsg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5733083 5740359 a 0 + 1 chr1 3155164 3159480 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpezqadf8_/f1.bed -b /tmp/tmpezqadf8_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3436267 3446267 a 0 + 1 chr16 8026421 8027505 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmppq6qpspd/f1.bed -b /tmp/tmppq6qpspd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 1983 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmprwh6q25m/f1.bed -b /tmp/tmprwh6q25m/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7237426 7239450 a 0 + 1 chr1 5282847 5290530 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpjznum1id/f1.bed -b /tmp/tmpjznum1id/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9086 a 0 + 1 chr1 1 9086 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmplxdkukaw/f1.bed -b /tmp/tmplxdkukaw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 1154 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpwi5w23hu/f1.bed -b /tmp/tmpwi5w23hu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3508648 3510286 a 0 + 1 chr2 990057 995110 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpvbbapc0l/f1.bed -b /tmp/tmpvbbapc0l/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 3337 a 0 - 1 chr1 1 3337 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp6fg6ecb8/f1.bed -b /tmp/tmp6fg6ecb8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8331845 8341438 a 0 + 1 chr1 66095 75688 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpngc6k4yi/f1.bed -b /tmp/tmpngc6k4yi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 8284 a 0 + 1 chr1 4662645 4666732 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfxffurbx/f1.bed -b /tmp/tmpfxffurbx/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 82 a 0 - 1 chr1 1 82 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpyhk2skyg/f1.bed -b /tmp/tmpyhk2skyg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1208883 1208884 a 0 + 1 chr16 4183010 4188076 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmploumvtfp/f1.bed -b /tmp/tmploumvtfp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5481810 5488186 a 0 - 1 chr2 6125241 6127806 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpl0d8f7vq/f1.bed -b /tmp/tmpl0d8f7vq/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 9797234 9803719 a 0 - 1 chr14 1393338 1403249 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp20h8hopv/f1.bed -b /tmp/tmp20h8hopv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1863892 1868901 a 0 - 1 chr22 1247745 1254708 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp6r4cob2y/f1.bed -b /tmp/tmp6r4cob2y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1571593 1576302 a 0 - 1 chr1 8630134 8630135 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpsb_qy6lw/f1.bed -b /tmp/tmpsb_qy6lw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr2 4240350 4249331 a 0 - 1 chr20 3805931 3814873 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpl_n3k2ma/f1.bed -b /tmp/tmpl_n3k2ma/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2826 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1w9kz6xs/f1.bed -b /tmp/tmp1w9kz6xs/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3098252 3105361 a 0 + 1 chr1 8327957 8336524 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_8_6bdl9/f1.bed -b /tmp/tmp_8_6bdl9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6295314 6303243 a 0 - 1 chr9 5878582 5879933 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp7sumk86y/f1.bed -b /tmp/tmp7sumk86y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4653187 4662659 a 0 - 1 chrM 3764362 3764570 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmplv8htvfl/f1.bed -b /tmp/tmplv8htvfl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6509348 6517817 a 0 + 1 chr1 5485255 5493452 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp2lg4k2uj/f1.bed -b /tmp/tmp2lg4k2uj/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6939028 6947352 a 0 + 1 chr1 6684269 6690737 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp9klklfgu/f1.bed -b /tmp/tmp9klklfgu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4612461 4620209 a 0 + 1 chr1 9428907 9433698 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmphccweapt/f1.bed -b /tmp/tmphccweapt/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7907578 7908190 a 0 + 1 chr18 7423599 7424615 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpr7stqln7/f1.bed -b /tmp/tmpr7stqln7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7907161 7907697 a 0 - 1 chr13 1393263 1397762 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmphzpmupwb/f1.bed -b /tmp/tmphzpmupwb/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 6390 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpjphi7t3a/f1.bed -b /tmp/tmpjphi7t3a/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 4030917 4034005 a 0 + 1 chr14 7744746 7747834 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp9ahx5lb8/f1.bed -b /tmp/tmp9ahx5lb8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 4484 a 0 + 1 chr1 1 4484 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp7_ruh35k/f1.bed -b /tmp/tmp7_ruh35k/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 5590 a 0 + 1 chr1 1 5590 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp584puqgm/f1.bed -b /tmp/tmp584puqgm/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2775531 2776185 a 0 - 1 chr10 6362981 6365131 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpr7iqjyh4/f1.bed -b /tmp/tmpr7iqjyh4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7960944 7963700 a 0 - 1 chr12 7960944 7967789 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp42ist77y/f1.bed -b /tmp/tmp42ist77y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 883630 890059 a 0 - 1 chr15 5120232 5121638 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpy0cstkso/f1.bed -b /tmp/tmpy0cstkso/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3915755 3921510 a 0 + 1 chr1 2307470 2313225 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpgghruxr_/f1.bed -b /tmp/tmpgghruxr_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 3379321 3380624 a 0 + 1 chr1 2613863 2615166 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpk3npzcny/f1.bed -b /tmp/tmpk3npzcny/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5493207 5502290 a 0 + 1 chr1 1202006 1211089 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp6ieenp0z/f1.bed -b /tmp/tmp6ieenp0z/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7013218 7015492 a 0 - 1 chr13 5073163 5076857 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpuuodrz4r/f1.bed -b /tmp/tmpuuodrz4r/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 7201585 7206125 a 0 + 1 chr1 1284757 1291920 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmptnwxadzk/f1.bed -b /tmp/tmptnwxadzk/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8047649 8052125 a 0 + 1 chr1 5315496 5316638 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmprsdiwy3d/f1.bed -b /tmp/tmprsdiwy3d/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 576499 579081 a 0 + 1 chr1 2817354 2817706 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpy85k_fsv/f1.bed -b /tmp/tmpy85k_fsv/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2194577 2199746 a 0 + 1 chr1 1710221 1718943 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmplv337u09/f1.bed -b /tmp/tmplv337u09/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr3 5368603 5369211 a 0 + 1 chr8 8635749 8639116 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpbcuyjnys/f1.bed -b /tmp/tmpbcuyjnys/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6314495 6318428 a 0 + 1 chr2 5472261 5477640 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_fq1xhku/f1.bed -b /tmp/tmp_fq1xhku/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 5798460 5806850 a 0 - 1 chrY 1221568 1231282 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp8m6ndr6c/f1.bed -b /tmp/tmp8m6ndr6c/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8405701 8406746 a 0 + 1 chr1 4715313 4720860 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpjels1bsg/f1.bed -b /tmp/tmpjels1bsg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8097885 8099183 a 0 - 1 chr10 5825944 5835014 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpq0xvh87y/f1.bed -b /tmp/tmpq0xvh87y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 2890467 2894291 a 0 + 1 chrY 957834 959044 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp1a7q6tky/f1.bed -b /tmp/tmp1a7q6tky/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 9114 a 0 + 1 chr1 1 9114 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp0hvsjp2y/f1.bed -b /tmp/tmp0hvsjp2y/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 7075 a 0 - 1 chr1 1 7075 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpzfuupdp2/f1.bed -b /tmp/tmpzfuupdp2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 6156850 6164480 a 0 + 1 chr1 4429277 4436907 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpefm11s_c/f1.bed -b /tmp/tmpefm11s_c/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 10001 a 0 - 1 chr1 1 10001 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpxjav_7eo/f1.bed -b /tmp/tmpxjav_7eo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 799 a 0 + 1 chr1 1 799 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpab005aiw/f1.bed -b /tmp/tmpab005aiw/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 8084634 8091279 a 0 + 1 chr11 325929 327273 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpdjwzk9yn/f1.bed -b /tmp/tmpdjwzk9yn/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpkxmkq3d9/f1.bed -b /tmp/tmpkxmkq3d9/f2.bed ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain149-method_chain149] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 192 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain210-method_chain210] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 150 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain183-method_chain183] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:140 E (and 117 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain189-method_chain189] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:21 E (and 95 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 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'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain131-method_chain131] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6822361 | 6831598 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6822361 | 6831598 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6822361 | 6831598 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6822361 | 6831598 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6822361 | 6822362 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges 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('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges 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('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain119-method_chain119] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 168 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/attr.py:65 | (and 259 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') __________ test_three_in_a_row[strandedness_chain154-method_chain154] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 124 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain198-method_chain198] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 195 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ___________ test_three_in_a_row[strandedness_chain90-method_chain90] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain229-method_chain229] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain211-method_chain211] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain184-method_chain184] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkdGQDYgZGR0YGBiCGIgYGACMIAlc=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain168-method_chain168] __________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 176 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGBEiTGARkBQYMgAAWa4EHg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 360, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | (and 280 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain190-method_chain190] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain91-method_chain91] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:21 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:37 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:43 E (and 38 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain199-method_chain199] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain155-method_chain155] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 106 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain133-method_chain133] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E (and 137 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain215-method_chain215] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain231-method_chain231] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E (and 132 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain219-method_chain219] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same'), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicJYiBCQAACMJcn/n/U1kyGE4MHsmBCKXOuend7Hi0f4kE5g==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain92-method_chain92] ___________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'same'), method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'same'), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain185-method_chain185] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGAAYigCscGQgREsARZhgkgBAFOiA90=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') __________ test_three_in_a_row[strandedness_chain200-method_chain200] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 195 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain156-method_chain156] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain232-method_chain232] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E (and 117 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain134-method_chain134] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E (and 117 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain157-method_chain157] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E /usr/lib/python3/dist-packages/pandas/core/common.py:143 E (and 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain120-method_chain120] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 183 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 | /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 | (and 83 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain238-method_chain238] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same'), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:21 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:37 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:43 E (and 39 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain186-method_chain186] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain201-method_chain201] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 135 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain169-method_chain169] __________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 183 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBhhIoxAggkuzgiGDABl+ARg') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 | (and 163 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 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('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain233-method_chain233] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain135-method_chain135] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain192-method_chain192] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 5682631 | 5685465 | a | 0 | + | E | chr1 | 9999999 | 10007495 | a | 0 | + | E | chr1 | 2811968 | 2814426 | a | 0 | + | E | chr1 | 6131340 | 6136389 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr1 | 9624417 | 9626875 | a | 0 | + | E | chr1 | 1251355 | 1254382 | a | 0 | + | E | chr1 | 1251355 | 1253488 | a | 0 | + | E | chr1 | 3290069 | 3297469 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 9492799 | 9493140 | a | 0 | + | E | chr1 | 1336846 | 1343602 | a | 0 | + | E | chr1 | 9533204 | 9537169 | a | 0 | - | E | chr1 | 1336846 | 1339251 | a | 0 | - | E | ... | ... | ... | ... | ... | ... | E | chr17 | 3558306 | 3564664 | a | 0 | - | E | chr17 | 4294229 | 4304170 | a | 0 | - | E | chr21 | 1336846 | 1344425 | a | 0 | - | E | chrM | 3331691 | 3334483 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3976382 | 3983009 | a | 0 | + | E | chr1 | 3089640 | 3096267 | a | 0 | - | E | chr10 | 7412158 | 7416599 | a | 0 | - | E | chr12 | 7507562 | 7514189 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 3 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'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') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9061678 | 9061680 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1251355 | 1254189 | a | 0 | ... | | chr1 | 1251355 | 1258851 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1251355 | 1254189 | a | 0 | ... | | chr1 | 1251355 | 1258851 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty 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Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty 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('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty 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('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain158-method_chain158] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain239-method_chain239] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain247-method_chain247] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain202-method_chain202] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same'), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain220-method_chain220] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same'), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEJGIMEEZDKC2YwQFgKBIQMAXGsEIA==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') __________ test_three_in_a_row[strandedness_chain217-method_chain217] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 7313845 | 7313846 | a | 0 | - | | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 180 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3S2Pi/L6Gx8IpaBwREIGR0ZnPNnbmVwZIQgRiAJloCJQHiOQHFHBgBeFwlj') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 | (and 217 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain194-method_chain194] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7415473 | 7421520 | a | 0 | ... | | chr1 | 7415473 | 7421520 | a | 0 | ... | | chr1 | 7415473 | 7421520 | a | 0 | ... | | chr1 | 7415473 | 7421520 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7415473 | 7425251 | a | 0 | ... | | chr1 | 7415473 | 7425251 | a | 0 | ... | | chr1 | 7415473 | 7425251 | a | 0 | ... | | chr1 | 7415473 | 7425251 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 27 rows and 11 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain248-method_chain248] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 195 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain159-method_chain159] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 106 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain170-method_chain170] __________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEJGIMEEZDKCGIxALkicEYZAbDBkAABpIQRi') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') __________ test_three_in_a_row[strandedness_chain203-method_chain203] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 114 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain121-method_chain121] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite'), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGGEijECCCSEOhgwAZhcEYQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') __________ test_three_in_a_row[strandedness_chain243-method_chain243] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same'), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') 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('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain234-method_chain234] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOGwJCBESHFBBEHAF5KBB8=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') __________ test_three_in_a_row[strandedness_chain136-method_chain136] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGAAYigCscGQgREmwQSRAwBLNgOe') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', 'opposite'), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 | /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') __________ test_three_in_a_row[strandedness_chain249-method_chain249] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain160-method_chain160] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain196-method_chain196] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 250 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain204-method_chain204] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 100 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain221-method_chain221] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGAAYkcmMMnICOYDIYQLYYAhAwBPNQPe') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') __________ test_three_in_a_row[strandedness_chain235-method_chain235] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3225276 | 3226820 | a | 0 | + | | chr1 | 6478741 | 6484325 | a | 0 | - | | chr1 | 9846150 | 9854763 | a | 0 | - | | chr1 | 5131458 | 5139661 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 5532821 | 5534365 | a | 0 | - | | chr5 | 6547328 | 6548872 | a | 0 | - | | chr12 | 3128686 | 3130335 | a | 0 | + | | chr14 | 6779489 | 6783636 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain171-method_chain171] __________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGBEiTGARkBQYMgAAWa4EHg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') __________ test_three_in_a_row[strandedness_chain255-method_chain255] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E /usr/lib/python3/dist-packages/pandas/core/common.py:143 E (and 63 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain250-method_chain250] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 131 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain205-method_chain205] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain245-method_chain245] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 242 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain197-method_chain197] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E (and 132 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain161-method_chain161] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:21 E (and 140 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain218-method_chain218] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 171 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGBEiTGARkBQYMgAAWa4EHg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 | /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 | (and 83 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges 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'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain122-method_chain122] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', 'opposite'), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') __________ test_three_in_a_row[strandedness_chain256-method_chain256] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain236-method_chain236] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3451390 | 3451391 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | | chr1 | 20 | 21 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | | chr2 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain251-method_chain251] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 195 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain206-method_chain206] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E /usr/lib/python3/dist-packages/pandas/core/common.py:143 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain246-method_chain246] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E (and 133 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain278-method_chain278] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain172-method_chain172] __________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBhhIoxAggkuzgiGDABl+ARg') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') __________ test_three_in_a_row[strandedness_chain162-method_chain162] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False) method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkdGQFYgYGRkdGBgYghiIGACGoAlY=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain257-method_chain257] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 102 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain264-method_chain264] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain237-method_chain237] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same'), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain252-method_chain252] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 126 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain207-method_chain207] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain285-method_chain285] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr2 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain222-method_chain222] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | | chr1 | 1 | 2 | a | 0 | - | | | chr1 | 1 | 2 | a | 0 | - | | | chr1 | 2191464 | 2191465 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 | (and 27 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3Q22MbB6MjI6JxS9YTR2bkigIHBEQgZHZmdFQsyGIFsRjgCqoPIwkQgPEeguCMDAOnnCuk=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'same'), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4042 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 6241 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 6241 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 6241 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 6241 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 6241 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain292-method_chain292] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain258-method_chain258] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain280-method_chain280] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E (and 137 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain286-method_chain286] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain253-method_chain253] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain173-method_chain173] __________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 | (and 30 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGBEiTGARkBQYMgAAWa4EHg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', False), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:373 | (and 23 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 9 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') __________ test_three_in_a_row[strandedness_chain298-method_chain298] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E (and 239 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain208-method_chain208] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 101 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain271-method_chain271] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 | (and 27 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGAAYkcmMMnACOYDIZgLRWDIAABPIwPe') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') 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('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain259-method_chain259] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/attr.py:11 E (and 328 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain281-method_chain281] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E (and 118 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain254-method_chain254] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain294-method_chain294] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E (and 279 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain287-method_chain287] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/attr.py:11 E (and 377 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain223-method_chain223] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same'), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGBEiTGARkBQYMgAAWa4EHg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') __________ test_three_in_a_row[strandedness_chain304-method_chain304] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 137 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain299-method_chain299] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 196 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain260-method_chain260] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain224-method_chain224] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 150 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain288-method_chain288] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain282-method_chain282] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain266-method_chain266] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 168 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwwQUYwZAAAWZwEHg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/attr.py:65 | (and 257 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty 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('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 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('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain295-method_chain295] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 199 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain305-method_chain305] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E (and 136 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain311-method_chain311] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEJGIMEEZDKC2VBBMJcJLsIIQwwAgvsEow==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8375584 | 8377211 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') __________ test_three_in_a_row[strandedness_chain300-method_chain300] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E (and 246 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain174-method_chain174] __________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', False), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', False), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGBEiTGARkBQYMgAAWa4EHg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') __________ test_three_in_a_row[strandedness_chain225-method_chain225] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'same') method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'same'), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain296-method_chain296] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E (and 239 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain306-method_chain306] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E (and 172 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain321-method_chain321] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') __________ test_three_in_a_row[strandedness_chain301-method_chain301] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 198 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain272-method_chain272] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBhhIoxAggkuzgiGDABl+ARg') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain313-method_chain313] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 8073 | a | 0 | + | | chr1 | 1 | 8073 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 8073 | a | 0 | + | | chr1 | 1 | 8073 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 8073 | a | 0 | + | | chr1 | 1 | 8073 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 8073 | a | 0 | + | | chr1 | 1 | 8073 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 8073 | a | 0 | + | | chr1 | 1 | 8073 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain297-method_chain297] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E (and 246 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain283-method_chain283] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGAAYigCsR2ZgJiBESwBFmGCyAIAU7oD3w==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3016961 | 3023471 | a | 0 | ... | | chr1 | 3016961 | 3023471 | a | 0 | ... | | chr1 | 3016961 | 3023471 | a | 0 | ... | | chr20 | 3016961 | 3023471 | a | 0 | ... | | chr20 | 3016961 | 3023471 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') __________ test_three_in_a_row[strandedness_chain307-method_chain307] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 136 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain322-method_chain322] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E (and 217 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain331-method_chain331] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain302-method_chain302] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E (and 175 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain273-method_chain273] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/attr.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/attr.py:18 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/attr.py:20 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/attr.py:23 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/attr.py:28 E (and 247 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain267-method_chain267] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 191 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwwQUYwZAAAWZwEHg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', 'opposite'), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 | /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 | (and 83 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') 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'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') __________ test_three_in_a_row[strandedness_chain290-method_chain290] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1019670 | 1019671 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 1019670 | 1019671 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E | chr2 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZHQuOLSO0YWhfedRRmdbAQNG58jr+xidHZ/8ZGBwBEJGR2Zn/n4xRkcmoFpHFhDBACawIUZUGbBCZmQtLFCaCUUhRBtQDcg+F4amK9swXAVyKMhNIMUQV4H0QN0EFoDbwgChKXI2BAHFIYEAFwEASu0sZg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty 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'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty 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('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 7082 | a | 0 | ... | | chr1 | 1 | 7082 | a | 0 | ... | | chr1 | 1 | 7082 | a | 0 | ... | | chr1 | 1 | 7082 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 7082 | a | 0 | ... | | chr1 | 1 | 7082 | a | 0 | ... | | chr1 | 1 | 7082 | a | 0 | ... | | chr1 | 1 | 7082 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 7082 | a | 0 | ... | | chr1 | 1 | 7082 | a | 0 | ... | | chr1 | 1 | 7082 | a | 0 | ... | | chr1 | 1 | 7082 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain284-method_chain284] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkdGQGYgZGR0YGBiCGIgYGACLGAlQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain327-method_chain327] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1762305 | 1766534 | a | 0 | - | | chr1 | 8154658 | 8161143 | a | 0 | - | | chr8 | 7807486 | 7808902 | a | 0 | - | | chr21 | 4371228 | 4380778 | a | 0 | - | | chrY | 1121174 | 1126983 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1762305 | 1766534 | a | 0 | - | | chr1 | 8154658 | 8161143 | a | 0 | - | | chr8 | 7807486 | 7808902 | a | 0 | - | | chr21 | 4371228 | 4380778 | a | 0 | - | | chrY | 1121174 | 1126983 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1762305 | 1766534 | a | 0 | - | | chr1 | 8154658 | 8161143 | a | 0 | - | | chr8 | 7807486 | 7808902 | a | 0 | - | | chr21 | 4371228 | 4380778 | a | 0 | - | | chrY | 1121174 | 1126983 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain274-method_chain274] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain308-method_chain308] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E (and 217 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain303-method_chain303] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E (and 136 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain323-method_chain323] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 108 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain316-method_chain316] __________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | (and 69 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZHRkZGBwBEJGIMEEZDKC2VBBMJcRwgBDBgBzHwSi') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 | (and 161 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') 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'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain341-method_chain341] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 155 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain315-method_chain315] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:12 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:101 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | (and 65 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 360, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | (and 279 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') __________ test_three_in_a_row[strandedness_chain348-method_chain348] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/init.py:174 E (and 186 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain268-method_chain268] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBhhIoxAggkuzgiGDABl+ARg') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') __________ test_three_in_a_row[strandedness_chain309-method_chain309] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 108 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain344-method_chain344] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/init.py:174 E (and 187 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain356-method_chain356] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E /usr/lib/python3/dist-packages/pandas/core/common.py:143 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain329-method_chain329] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 202 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain336-method_chain336] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E (and 275 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain325-method_chain325] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIMORCchghIkwOoIEwOJQQUYYYgAAgvgEow==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 7632944 | 7634211 | a | 0 | ... | | chr21 | 6369648 | 6370205 | a | 0 | ... | | chr22 | 1687363 | 1687898 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 7632944 | 7634211 | a | 0 | ... | | chr21 | 6369648 | 6370205 | a | 0 | ... | | chr22 | 1687363 | 1687898 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain349-method_chain349] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 178 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain332-method_chain332] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 5130797 | 5130798 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEQAwwZGCESzn7eelCJAFrrATi') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | (and 24 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain352-method_chain352] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 64 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain343-method_chain343] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 242 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain337-method_chain337] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 113 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain345-method_chain345] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 181 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain330-method_chain330] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E (and 187 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain333-method_chain333] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain357-method_chain357] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:21 E (and 141 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain353-method_chain353] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E /usr/lib/python3/dist-packages/pandas/core/common.py:143 E (and 62 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain350-method_chain350] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 126 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain317-method_chain317] __________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'overlap') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain269-method_chain269] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBhhIoxAggkuzgiGDABl+ARg') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') __________ test_three_in_a_row[strandedness_chain334-method_chain334] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9247554 | 9249475 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9677894 | 9677895 | a | 0 | + | | chr1 | 9677894 | 9677895 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr3 | 1 | 2 | a | 0 | + | | chr3 | 1 | 2 | a | 0 | + | | chr3 | 1 | 2 | a | 0 | + | | chr3 | 1 | 2 | a | 0 | + | | chr14 | 1 | 2 | a | 0 | + | | chr18 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain358-method_chain358] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain346-method_chain346] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 182 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain354-method_chain354] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain351-method_chain351] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 107 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain318-method_chain318] __________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') __________ test_three_in_a_row[strandedness_chain366-method_chain366] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGGEijECCCSEOhgwAZhcEYQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') __________ test_three_in_a_row[strandedness_chain335-method_chain335] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain360-method_chain360] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 88689 | 88690 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 88689 | 88690 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3TOjWRidGHoj3YAkq0bZEDsRW8ZHRmBjM7rqxidaw/HMjA6sjkyOIIoMGIFyjqClDgygQhmMJcRpAKkBhmxODKCdDkzRhVCdYAVs0J1ICMmiBGMcN1ANhgxQByD7kIXhgl9r6joSCaIIxng2tDdwADWChcBAOX5Lyc=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty 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'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7982 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7982 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7982 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7982 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7982 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7982 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7982 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain347-method_chain347] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 184 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain372-method_chain372] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 109 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain355-method_chain355] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None) method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E (and 106 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain369-method_chain369] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 | (and 24 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr17 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') __________ test_three_in_a_row[strandedness_chain364-method_chain364] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 180 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGMEIIsgIJJgQUmDIAABzGwSk') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 360, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | (and 282 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty 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('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 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PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain383-method_chain383] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5466333 | 5466334 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5466333 | 5466334 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5466333 | 5466334 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5466333 | 5466334 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5466333 | 5466334 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain270-method_chain270] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGBEiTGARkBQYMgAAWa4EHg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 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('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') __________ test_three_in_a_row[strandedness_chain381-method_chain381] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGAAYigCskGQEQgZGMFSYDEmiCQAXTsEHQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') __________ test_three_in_a_row[strandedness_chain378-method_chain378] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 133 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain319-method_chain319] __________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = (False, None), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=(False, None), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 28 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') __________ test_three_in_a_row[strandedness_chain385-method_chain385] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:21 E (and 95 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain362-method_chain362] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:373 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain367-method_chain367] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGBEiTHBBMGQAAFm4BB8=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +13 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 18 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 18 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 13 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance, ... (+ 6 more.) ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +13 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 18 | a | 0 | ... | | chr1 | 1 | 18 | a | 0 | ... | | chr1 | 1 | 18 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 18 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 13 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance, ... (+ 6 more.) ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') __________ test_three_in_a_row[strandedness_chain384-method_chain384] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +6 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 11 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 6 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain382-method_chain382] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain370-method_chain370] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') __________ test_three_in_a_row[strandedness_chain379-method_chain379] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None) method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:140 E (and 118 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain376-method_chain376] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain386-method_chain386] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain365-method_chain365] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 171 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('same', None), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 | (and 157 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') __________ test_three_in_a_row[strandedness_chain374-method_chain374] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2066450 | 2067074 | a | 0 | + | E | chr1 | 8585345 | 8586266 | a | 0 | + | E | chr1 | 1539710 | 1539711 | a | 0 | + | E | chr1 | 5626983 | 5634347 | a | 0 | - | E | ... | ... | ... | ... | ... | ... | E | chr17 | 9999999 | 10002890 | a | 0 | + | E | chr19 | 5355895 | 5357487 | a | 0 | + | E | chrX | 8160913 | 8169076 | a | 0 | + | E | chrX | 10000000 | 10004768 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2066450 | 2075154 | a | 0 | + | E | chr1 | 8585345 | 8586266 | a | 0 | + | E | chr2 | 5626983 | 5634347 | a | 0 | - | E | chr5 | 1539710 | 1539711 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr17 | 9999999 | 10002890 | a | 0 | + | E | chr19 | 5355895 | 5357487 | a | 0 | + | E | chrX | 8160913 | 8169076 | a | 0 | + | E | chrX | 10000000 | 10004768 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 7 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 6934163 | 6934505 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:104 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:106 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:12 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/join.py:14 E (and 47 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicnVE9SwNBEJ25j707FJErYiMETrFKYyeCxe5cIVhZXFobQRQEsdEiJJGAH0UKFUS7gK1/wM7CVn+BnX/E2dkk3BXqERhmZndm572dhzn08wKp9TaPOdztDZE2M0Rabx0hFfsfSNnpFVI8PEdqv4yQVrY7gNrXoDkkHBqokUNqHaKOOCyiDl3Fc31sscuU7YGaxi/0Ao/M4fGhx29zGMAF6oC2nhMGt9d9nkxL3S6ToN3XM7Tjp+ZTY3DMJKj4OqhWpgbUvE5/xafO5S3jm7kd9jzILL8zDeM/cdF4JzzBqA3pDU3zmwHN2k1pQGLSEXv7eYbyxBSfBDmRD9p764JSh5YF81nZlc0mkF13UFMglM/FQkn0UZKGjqMkIPVQ+LnEVmfRJxYwB1nVJ5pMV5K4lrE+/oSia0ocx7/0CUr6RFV9HHu/hj4mA/hXIFrt+SDLtZ4OP+9tNNgeX/4APpmGjQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges 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'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain380-method_chain380] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:293 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGQAEgxAJgwxMAAAKV8Ckg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain395-method_chain395] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 197 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain371-method_chain371] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E (and 217 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain399-method_chain399] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 123 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain320-method_chain320] __________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=(False, None), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | (and 24 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain393-method_chain393] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/init.py:174 E (and 199 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain403-method_chain403] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E /usr/lib/python3/dist-packages/natsort/utils.py:344 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain392-method_chain392] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 261 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain405-method_chain405] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain390-method_chain390] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain388-method_chain388] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3996087 | 4004725 | a | 0 | + | E | chr1 | 9119589 | 9122999 | a | 0 | + | E | chr1 | 8023078 | 8025559 | a | 0 | + | E | chr1 | 2920654 | 2924776 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr1 | 2920654 | 2924776 | a | 0 | + | E | chr1 | 10000000 | 10001865 | a | 0 | - | E | chr1 | 830815 | 832855 | a | 0 | - | E | chr1 | 10000000 | 10004122 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 3 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 9999999 | 10007893 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3807009 | 3816718 | a | 0 | + | E | chrY | 7040714 | 7050714 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicZVHPK0RxEJ95++Pty8q27/BKlvbASzk44/L9zlOcFFFOUpxsTlKkOIrLtkr+CQdFbi6iOGgP2rOrg3LDzcy897Wkppn5fub354u0Fr4iVS5bSLXoHo2HNL23iLT9fIW0OvSCZBZ2kEbbVY31VDuAJm/AsPENosmxH6IAArEUBWXrZQGVUgai2AJHyi6SSmBQdAJnpwfck2ofD4zT1Nc1N6LG+Az3pd3GyK+SfJYMf6WQwGH7zr0wgeN4nefTWPPpX25XgMrnKzzYDtyy5jrbO6+7ejbu46bWX+IsW79JR1t/1pX61v/k5Wxw0W1mK/2Y8uGJyule6fnKhSNKYKHVFNVRPgOdqgKqS8I3s0NbzTkpVKZAjt8Xxw52gDE+9Og9RFo+mUznmMjlIm1sPgJNRHW5K67oXWCH3wB/Pg3c78A3j9tVfg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10001828 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10001828 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges 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Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') 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'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 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Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain368-method_chain368] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('same', None), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('same', None), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBgRIkwQESAJhgwAWZIEHQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges 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'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') 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PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain396-method_chain396] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 195 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain404-method_chain404] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 107 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain394-method_chain394] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 195 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain407-method_chain407] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('overlap', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 106 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain400-method_chain400] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:140 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E (and 103 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain397-method_chain397] __________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'subtract'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/init.py:174 E (and 199 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain406-method_chain406] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('overlap', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:21 E (and 141 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain401-method_chain401] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:4162 E /usr/lib/python3/dist-packages/natsort/utils.py:329 E (and 65 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain402-method_chain402] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'nearest'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E /usr/lib/python3/dist-packages/pandas/core/array_algos/take.py:574 E (and 61 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain411-method_chain411] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('overlap', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 109 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain421-method_chain421] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('intersect', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 E (and 23 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain398-method_chain398] __________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('set_union', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E (and 194 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain420-method_chain420] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('intersect', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:21 E (and 142 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain432-method_chain432] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr7 | 1 | 2 | a | 0 | + | | chr8 | 1 | 2 | a | 0 | + | | chr13 | 1 | 2 | a | 0 | + | | chr15 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain428-method_chain428] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'set_intersect'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E (and 120 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain409-method_chain409] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('overlap', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr1 | 7159867 | 7159868 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E | chr13 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 7159867 | 7159868 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E | chr13 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3Su+T+H0dlicjGjM9u1IEYXhunmDIzO2rwxDIyOLI4MjjyMjsyOjEACjBhATEYQwYCKmBwZQaRzroM1VAMTMgLqA2tlAallAZkD0gYiaWE/E1QNWCM6YoAhRrAWBhBkgAkyAADh4iR1') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges 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'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty 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'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges 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PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain417-method_chain417] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('nearest', 'intersect'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RhmPjXjIHBkRGGGBiBJJACMRgcmRBSYMgAAKupBeY=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges 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'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain415-method_chain415] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('nearest', 'overlap'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGBEiTGARkBQYMgAAWa4EHg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') __________ test_three_in_a_row[strandedness_chain431-method_chain431] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'intersect'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:293 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkdOQCYgZGR0YGBiCGIgYGACNgAls=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain427-method_chain427] __________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'set_union'), E gr=Empty PyRanges, # or any other generated value E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:112 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:117 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:342 E (and 132 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain433-method_chain433] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'join'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E (and 19 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain413-method_chain413] __________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'set_union'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 180 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGAAYihiYATzgZDBkQkuDoYMAE8RA94=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3784, in set_union | gr = gr.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 360, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'set_union'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | (and 280 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty 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'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') 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('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain434-method_chain434] __________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('join', 'set_union'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:33 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:41 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:13 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:17 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:21 E (and 95 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain414-method_chain414] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'set_intersect'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:39 | (and 171 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGBEiTGARkBQYMgAAWa4EHg==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3688, in set_intersect | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'set_intersect'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 | (and 163 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkAEJGIGRgAJIMQDYMMQAAKBUCkg==') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') _______________________________ test_merge[True] _______________________________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strand = True @pytest.mark.bedtools > @pytest.mark.parametrize("strand", [True, False]) tests/test_unary.py:31: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:75: in test_merge result = gr.merge(strand=strand, count=True) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_merge( E strand=True, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp44c8kpvj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 485517 | 490073 | a | 0 | - | | chr1 | 3914259 | 3916679 | a | 0 | - | | chr5 | 6487836 | 6489768 | a | 0 | - | | chr7 | 9880790 | 9886770 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr7 | 485517 | 494172 | a | 0 | - | | chr7 | 318314 | 318433 | a | 0 | - | | chr7 | 1005411 | 1014738 | a | 0 | - | | chr7 | 7203182 | 7213182 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpgc1j4494/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 485517 490073 - 1 chr1 3914259 3916679 - 1 chr5 6487836 6489768 - 1 chr7 318314 318433 - 1 chr7 485517 494172 - 1 chr7 1005411 1014738 - 1 chr7 7203182 7213182 - 2 chr7 9323447 9332871 + 1 chr7 9858919 9866464 - 1 chr7 9880790 9886770 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 485517 490073 - 1 1 chr1 3914259 3916679 - 1 2 chr5 6487836 6489768 - 1 3 chr7 318314 318433 - 1 4 chr7 485517 494172 - 1 5 chr7 1005411 1014738 - 1 6 chr7 7203182 7213182 - 2 7 chr7 9323447 9332871 + 1 8 chr7 9858919 9866464 - 1 9 chr7 9880790 9886770 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8655 | 11234 | a | 0 | + | | chr1 | 8655 | 11234 | a | 0 | + | | chr1 | 8655 | 11234 | a | 0 | + | | chr1 | 8655 | 11234 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 8655 | 8656 | a | 0 | + | | chr1 | 8655 | 11234 | a | 0 | + | | chr1 | 8655 | 11234 | a | 0 | + | | chr1 | 8655 | 11234 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpytqwcxot/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8655 13211 + 11 bedtools_df Chromosome Start End Strand Count 0 chr1 8655 13211 + 11 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8655 | 11234 | a | 0 | + | | chr1 | 8655 | 11234 | a | 0 | + | | chr1 | 8655 | 11234 | a | 0 | + | | chr1 | 8655 | 11234 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 8655 | 11234 | a | 0 | + | | chr1 | 8655 | 8656 | a | 0 | + | | chr1 | 8655 | 11234 | a | 0 | + | | chr1 | 8655 | 11234 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpctxbl608/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8655 13211 + 10 bedtools_df Chromosome Start End Strand Count 0 chr1 8655 13211 + 10 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmplcnpo32w/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 9 chr1 1 2 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 9 1 chr1 1 2 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpmpju6g03/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 8 chr1 1 2 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 8 1 chr1 1 2 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp7ca8zhhm/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 7 chr1 1 2 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 7 1 chr1 1 2 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmphffl9pz_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 7 chr1 1 2 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 7 1 chr1 1 2 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6452548 | 6452656 | a | 0 | + | | chr1 | 4753198 | 4759657 | a | 0 | + | | chr1 | 7464876 | 7469727 | a | 0 | + | | chr1 | 3834132 | 3838983 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 9999999 | 10008273 | a | 0 | - | | chr7 | 925683 | 925781 | a | 0 | + | | chr11 | 4990918 | 4995399 | a | 0 | + | | chr19 | 8149329 | 8152101 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpcl9s9hs9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2507681 2515136 - 2 chr1 3399260 3409081 - 1 chr1 3834132 3838983 + 1 chr1 4753198 4759657 + 1 chr1 6452548 6452656 + 1 chr1 7464876 7469727 + 1 chr11 4990918 4995399 + 1 chr19 8149329 8152101 + 1 chr6 9999999 10008273 - 1 chr7 925683 925781 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2507681 2515136 - 2 1 chr1 3399260 3409081 - 1 2 chr1 3834132 3838983 + 1 3 chr1 4753198 4759657 + 1 4 chr1 6452548 6452656 + 1 5 chr1 7464876 7469727 + 1 6 chr11 4990918 4995399 + 1 7 chr19 8149329 8152101 + 1 8 chr6 9999999 10008273 - 1 9 chr7 925683 925781 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr11 | 1 | 2 | a | 0 | + | | chr11 | 1 | 2 | a | 0 | + | | chr11 | 1 | 2 | a | 0 | + | | chr11 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp3gp5iizo/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 4 chr11 1 2 + 4 chr6 1 2 + 1 chr7 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 4 1 chr11 1 2 + 4 2 chr6 1 2 + 1 3 chr7 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpubbyrgbg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp27x221cx/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpunwn8bwj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5415162 | 5421719 | a | 0 | + | | chr1 | 2080894 | 2081743 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpb1wm0wq5/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2080894 2081743 + 1 chr1 5415162 5421719 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2080894 2081743 + 1 1 chr1 5415162 5421719 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8840065 | 8843222 | a | 0 | - | | chr2 | 2452007 | 2456351 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpw5ki24s1/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8840065 8843222 - 1 chr2 2452007 2456351 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 8840065 8843222 - 1 1 chr2 2452007 2456351 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6926761 | 6927473 | a | 0 | + | | chr2 | 892533 | 901109 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpo1qliewr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6926761 6927473 + 1 chr2 892533 901109 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6926761 6927473 + 1 1 chr2 892533 901109 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6522380 | 6523567 | a | 0 | + | | chr1 | 7132131 | 7141324 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpl4x6emq8/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6522380 6523567 + 1 chr1 7132131 7141324 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6522380 6523567 + 1 1 chr1 7132131 7141324 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 8174 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpp5ohfia3/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 8174 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 8174 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3901103 | 3910348 | a | 0 | - | | chr20 | 9842413 | 9844944 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp0s95psji/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3901103 3910348 - 1 chr20 9842413 9844944 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3901103 3910348 - 1 1 chr20 9842413 9844944 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2135436 | 2136942 | a | 0 | + | | chrM | 1140055 | 1143660 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpe679fwvw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2135436 2136942 + 1 chrM 1140055 1143660 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2135436 2136942 + 1 1 chrM 1140055 1143660 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9089129 | 9098466 | a | 0 | - | | chr19 | 5721743 | 5731105 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpiq1oq2gq/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9089129 9098466 - 1 chr19 5721743 5731105 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 9089129 9098466 - 1 1 chr19 5721743 5731105 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5870576 | 5875015 | a | 0 | - | | chr7 | 2602798 | 2606720 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpdekat9f4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5870576 5875015 - 1 chr7 2602798 2606720 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5870576 5875015 - 1 1 chr7 2602798 2606720 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2072931 | 2075108 | a | 0 | - | | chr1 | 6534730 | 6541150 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpz6feurkf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2072931 2075108 - 1 chr1 6534730 6541150 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2072931 2075108 - 1 1 chr1 6534730 6541150 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7853805 | 7862043 | a | 0 | + | | chr1 | 4236601 | 4242143 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp1p5xqd6k/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4236601 4242143 - 1 chr1 7853805 7862043 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4236601 4242143 - 1 1 chr1 7853805 7862043 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9490085 | 9493202 | a | 0 | + | | chr13 | 9923293 | 9932083 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpi36ogcrk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9490085 9493202 + 1 chr13 9923293 9932083 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 9490085 9493202 + 1 1 chr13 9923293 9932083 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4301107 | 4301131 | a | 0 | - | | chr15 | 1028022 | 1036392 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmptxe_d_j7/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4301107 4301131 - 1 chr15 1028022 1036392 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4301107 4301131 - 1 1 chr15 1028022 1036392 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 809402 | 816740 | a | 0 | + | | chr1 | 821910 | 824729 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp5t66_2ol/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 809402 816740 + 1 chr1 821910 824729 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 809402 816740 + 1 1 chr1 821910 824729 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1654255 | 1657693 | a | 0 | + | | chr1 | 9518671 | 9525205 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpv0nnxlnq/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1654255 1657693 + 1 chr1 9518671 9525205 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1654255 1657693 + 1 1 chr1 9518671 9525205 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 1196 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpye9e3zyq/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 1196 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 1196 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1526022 | 1531690 | a | 0 | + | | chr1 | 5572813 | 5581021 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp19mrx8nk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1526022 1531690 + 1 chr1 5572813 5581021 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1526022 1531690 + 1 1 chr1 5572813 5581021 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2246399 | 2250398 | a | 0 | + | | chr9 | 7940891 | 7941821 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp_o9ntibt/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2246399 2250398 + 1 chr9 7940891 7941821 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2246399 2250398 + 1 1 chr9 7940891 7941821 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6152789 | 6161236 | a | 0 | - | | chr1 | 1803050 | 1810981 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp3sv_ipwi/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1803050 1810981 - 1 chr1 6152789 6161236 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1803050 1810981 - 1 1 chr1 6152789 6161236 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 7451 | a | 0 | + | | chr1 | 1 | 7451 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpvfme5vm9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 7451 + 1 chr1 1 7451 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 7451 + 1 1 chr1 1 7451 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6978623 | 6987594 | a | 0 | + | | chr10 | 6978623 | 6978641 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmphmra53co/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6978623 6987594 + 1 chr10 6978623 6978641 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6978623 6987594 + 1 1 chr10 6978623 6978641 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4190640 | 4198076 | a | 0 | + | | chr1 | 499108 | 503594 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpep1w_9lr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 499108 503594 - 1 chr1 4190640 4198076 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 499108 503594 - 1 1 chr1 4190640 4198076 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7495740 | 7503854 | a | 0 | + | | chr2 | 2530399 | 2534045 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmppn4_eru9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7495740 7503854 + 1 chr2 2530399 2534045 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 7495740 7503854 + 1 1 chr2 2530399 2534045 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 1075 | a | 0 | + | | chr1 | 1 | 1075 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp97iwy7sq/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 1075 + 2 bedtools_df Chromosome Start End Strand Count 0 chr1 1 1075 + 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 9334 | a | 0 | + | | chr1 | 1 | 9334 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpz4tg79nr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 9334 + 2 bedtools_df Chromosome Start End Strand Count 0 chr1 1 9334 + 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7483362 | 7487178 | a | 0 | + | | chr1 | 4062742 | 4072232 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpvc0t2wyp/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4062742 4072232 - 1 chr1 7483362 7487178 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4062742 4072232 - 1 1 chr1 7483362 7487178 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4737911 | 4738077 | a | 0 | + | | chr1 | 8900695 | 8908371 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp5eswvbhj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4737911 4738077 + 1 chr1 8900695 8908371 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4737911 4738077 + 1 1 chr1 8900695 8908371 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6972470 | 6979375 | a | 0 | + | | chr1 | 4700792 | 4708025 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp28j79k84/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4700792 4708025 + 1 chr1 6972470 6979375 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4700792 4708025 + 1 1 chr1 6972470 6979375 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9549717 | 9559106 | a | 0 | + | | chr1 | 8200208 | 8206951 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp4pbus8ic/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8200208 8206951 + 1 chr1 9549717 9559106 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 8200208 8206951 + 1 1 chr1 9549717 9559106 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1602855 | 1608578 | a | 0 | - | | chr8 | 8990611 | 8995711 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpfa4swexd/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1602855 1608578 - 1 chr8 8990611 8995711 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1602855 1608578 - 1 1 chr8 8990611 8995711 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4983760 | 4990004 | a | 0 | + | | chr6 | 9093025 | 9100423 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp2siy1ps_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4983760 4990004 + 1 chr6 9093025 9100423 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4983760 4990004 + 1 1 chr6 9093025 9100423 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 3837 | a | 0 | + | | chr1 | 6659914 | 6660471 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpy8m4av_v/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2 3837 + 1 chr1 6659914 6660471 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2 3837 + 1 1 chr1 6659914 6660471 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp5y3297bu/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3373994 | 3375535 | a | 0 | - | | chr16 | 7689785 | 7699779 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpr650rqwg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3373994 3375535 - 1 chr16 7689785 7699779 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3373994 3375535 - 1 1 chr16 7689785 7699779 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3128361 | 3133245 | a | 0 | - | | chr14 | 3917002 | 3924670 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmplfqolsjj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3128361 3133245 - 1 chr14 3917002 3924670 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3128361 3133245 - 1 1 chr14 3917002 3924670 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6303196 | 6312539 | a | 0 | + | | chr1 | 4515138 | 4524481 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp_fla0y__/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4515138 4524481 - 1 chr1 6303196 6312539 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4515138 4524481 - 1 1 chr1 6303196 6312539 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 10000 | a | 0 | + | | chr1 | 1 | 10000 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp_9biyfam/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 10000 + 1 chr1 1 10000 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 10000 + 1 1 chr1 1 10000 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 7778 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp79t8dtiu/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 7778 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 7778 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9114173 | 9121091 | a | 0 | + | | chr2 | 3027878 | 3032370 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp79t2qt2d/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9114173 9121091 + 1 chr2 3027878 3032370 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 9114173 9121091 + 1 1 chr2 3027878 3032370 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1170655 | 1180377 | a | 0 | + | | chr1 | 869993 | 879203 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp263jr8j6/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 869993 879203 - 1 chr1 1170655 1180377 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 869993 879203 - 1 1 chr1 1170655 1180377 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3202608 | 3204123 | a | 0 | + | | chr1 | 2632264 | 2633610 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmplzmwizsp/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2632264 2633610 + 1 chr1 3202608 3204123 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2632264 2633610 + 1 1 chr1 3202608 3204123 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7367303 | 7374300 | a | 0 | + | | chr4 | 4188114 | 4193160 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpj1laoux5/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7367303 7374300 + 1 chr4 4188114 4193160 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 7367303 7374300 + 1 1 chr4 4188114 4193160 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 7343 | a | 0 | + | | chr21 | 6047534 | 6056217 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmptlaeusvt/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 7343 + 1 chr21 6047534 6056217 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 7343 + 1 1 chr21 6047534 6056217 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4126984 | 4132326 | a | 0 | + | | chr10 | 8527169 | 8534390 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpxsc6sbbn/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4126984 4132326 + 1 chr10 8527169 8534390 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4126984 4132326 + 1 1 chr10 8527169 8534390 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 406978 | 412581 | a | 0 | + | | chr1 | 1773407 | 1781461 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpgyzve20e/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 406978 412581 + 1 chr1 1773407 1781461 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 406978 412581 + 1 1 chr1 1773407 1781461 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9352949 | 9353596 | a | 0 | + | | chr21 | 7150052 | 7156491 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp3g4hozyw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9352949 9353596 + 1 chr21 7150052 7156491 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 9352949 9353596 + 1 1 chr21 7150052 7156491 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3155479 | 3163056 | a | 0 | + | | chr16 | 9010313 | 9011495 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpn8zmld6t/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3155479 3163056 + 1 chr16 9010313 9011495 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3155479 3163056 + 1 1 chr16 9010313 9011495 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10001833 | a | 0 | + | | chr8 | 1163909 | 1165742 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp6zljgltp/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 10000000 10001833 + 1 chr8 1163909 1165742 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 10000000 10001833 + 1 1 chr8 1163909 1165742 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 9460 | a | 0 | - | | chr1 | 1 | 9460 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp0c76pa4k/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 9460 - 2 bedtools_df Chromosome Start End Strand Count 0 chr1 1 9460 - 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4252658 | 4255953 | a | 0 | - | | chr1 | 10000000 | 10003295 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpetr_yn4y/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4252658 4255953 - 1 chr1 10000000 10003295 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4252658 4255953 - 1 1 chr1 10000000 10003295 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5405349 | 5411896 | a | 0 | - | | chr2 | 7281045 | 7287592 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpx1oded6h/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5405349 5411896 - 1 chr2 7281045 7287592 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5405349 5411896 - 1 1 chr2 7281045 7287592 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7334098 | 7338675 | a | 0 | - | | chr1 | 2123078 | 2127655 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp03yzbwl_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2123078 2127655 - 1 chr1 7334098 7338675 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2123078 2127655 - 1 1 chr1 7334098 7338675 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1075077 | 1079883 | a | 0 | + | | chrX | 9331352 | 9332566 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp1wncazl6/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1075077 1079883 + 1 chrX 9331352 9332566 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1075077 1079883 + 1 1 chrX 9331352 9332566 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4829 | a | 0 | + | | chr1 | 1 | 4829 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpci93hoyf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 4829 + 2 bedtools_df Chromosome Start End Strand Count 0 chr1 1 4829 + 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5501929 | 5503057 | a | 0 | + | | chr3 | 2793380 | 2801042 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmps9ubd6pg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5501929 5503057 + 1 chr3 2793380 2801042 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5501929 5503057 + 1 1 chr3 2793380 2801042 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 6370 | a | 0 | + | | chr1 | 6649573 | 6652844 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmps276nhdh/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 6370 + 1 chr1 6649573 6652844 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 6370 + 1 1 chr1 6649573 6652844 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2999 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmphfnty_z1/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2999 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2999 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2441139 | 2443993 | a | 0 | - | | chr12 | 3956895 | 3957189 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp3wa4hq_f/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2441139 2443993 - 1 chr12 3956895 3957189 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2441139 2443993 - 1 1 chr12 3956895 3957189 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2497 | a | 0 | + | | chr1 | 1 | 2497 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp4qkrwsjg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2497 + 2 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2497 + 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6308689 | 6317304 | a | 0 | - | | chr17 | 3491649 | 3498052 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpr1jj2umt/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6308689 6317304 - 1 chr17 3491649 3498052 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6308689 6317304 - 1 1 chr17 3491649 3498052 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1707183 | 1715789 | a | 0 | - | | chr3 | 3667874 | 3675060 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpdkvo_4m6/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1707183 1715789 - 1 chr3 3667874 3675060 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1707183 1715789 - 1 1 chr3 3667874 3675060 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 5073 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmphzvg7ziw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 5073 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 5073 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6891040 | 6901040 | a | 0 | + | | chr1 | 8030350 | 8040319 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmptyfkt7dz/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6891040 6901040 + 1 chr1 8030350 8040319 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6891040 6901040 + 1 1 chr1 8030350 8040319 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8227828 | 8230763 | a | 0 | + | | chr18 | 8692096 | 8699073 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpzehomgvp/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8227828 8230763 + 1 chr18 8692096 8699073 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 8227828 8230763 + 1 1 chr18 8692096 8699073 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9999999 | 10006851 | a | 0 | + | | chr1 | 452120 | 461654 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp41o800t9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 452120 461654 - 1 chr1 9999999 10006851 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 452120 461654 - 1 1 chr1 9999999 10006851 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5378504 | 5386641 | a | 0 | + | | chr1 | 3444651 | 3446175 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp8jq8sadc/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3444651 3446175 - 1 chr1 5378504 5386641 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3444651 3446175 - 1 1 chr1 5378504 5386641 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4405077 | 4413125 | a | 0 | - | | chrX | 3563622 | 3566918 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp4tm3tkfc/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4405077 4413125 - 1 chrX 3563622 3566918 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4405077 4413125 - 1 1 chrX 3563622 3566918 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3449292 | 3454890 | a | 0 | - | | chr1 | 5966381 | 5974687 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpjv6v1rym/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3449292 3454890 - 1 chr1 5966381 5974687 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3449292 3454890 - 1 1 chr1 5966381 5974687 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6009265 | 6014784 | a | 0 | + | | chr20 | 6009265 | 6009993 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp7mpsht6t/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6009265 6014784 + 1 chr20 6009265 6009993 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6009265 6014784 + 1 1 chr20 6009265 6009993 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9999999 | 10006532 | a | 0 | + | | chr1 | 8713485 | 8714727 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpxsp5xewg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8713485 8714727 + 1 chr1 9999999 10006532 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 8713485 8714727 + 1 1 chr1 9999999 10006532 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6072780 | 6078070 | a | 0 | - | | chr1 | 4035712 | 4038204 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpaud41f24/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4035712 4038204 - 1 chr1 6072780 6078070 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4035712 4038204 - 1 1 chr1 6072780 6078070 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9999999 | 10001817 | a | 0 | + | | chr1 | 7121778 | 7121846 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpfgntqyq2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7121778 7121846 + 1 chr1 9999999 10001817 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 7121778 7121846 + 1 1 chr1 9999999 10001817 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6054916 | 6061380 | a | 0 | + | | chr1 | 1744639 | 1753348 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpicmt22pk/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1744639 1753348 - 1 chr1 6054916 6061380 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1744639 1753348 - 1 1 chr1 6054916 6061380 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7894050 | 7897824 | a | 0 | - | | chr9 | 5108516 | 5112170 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpjf9q_nwa/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7894050 7897824 - 1 chr9 5108516 5112170 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 7894050 7897824 - 1 1 chr9 5108516 5112170 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5298685 | 5303868 | a | 0 | + | | chr1 | 8438715 | 8441265 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpor2xbh3o/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5298685 5303868 + 1 chr1 8438715 8441265 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5298685 5303868 + 1 1 chr1 8438715 8441265 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 483280 | 488889 | a | 0 | - | | chr1 | 6266417 | 6266418 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmprm0h_pur/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 483280 488889 - 1 chr1 6266417 6266418 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 483280 488889 - 1 1 chr1 6266417 6266418 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 1377 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmprdci4mq_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr2 1 1377 + 1 bedtools_df Chromosome Start End Strand Count 0 chr2 1 1377 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6863487 | 6870051 | a | 0 | + | | chr1 | 4528941 | 4529812 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpnvqws657/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4528941 4529812 - 1 chr1 6863487 6870051 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4528941 4529812 - 1 1 chr1 6863487 6870051 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5448783 | 5453642 | a | 0 | + | | chr1 | 9857459 | 9857964 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpqi9n2iyc/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5448783 5453642 + 1 chr1 9857459 9857964 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5448783 5453642 + 1 1 chr1 9857459 9857964 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3671189 | 3676661 | a | 0 | + | | chr4 | 4251484 | 4252140 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpjklfuejq/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3671189 3676661 + 1 chr4 4251484 4252140 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 3671189 3676661 + 1 1 chr4 4251484 4252140 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmps4y6veo4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 - 2 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 - 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 850657 | 859405 | a | 0 | - | | chr4 | 2427268 | 2427539 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp54ia8t02/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 850657 859405 - 1 chr4 2427268 2427539 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 850657 859405 - 1 1 chr4 2427268 2427539 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4975175 | 4976647 | a | 0 | + | | chr1 | 9799671 | 9803166 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpmqcmf6f9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4975175 4976647 + 1 chr1 9799671 9803166 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4975175 4976647 + 1 1 chr1 9799671 9803166 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4858427 | 4862093 | a | 0 | + | | chr1 | 6602179 | 6607578 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp1zxwth44/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4858427 4862093 + 1 chr1 6602179 6607578 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4858427 4862093 + 1 1 chr1 6602179 6607578 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 503567 | 505146 | a | 0 | - | | chr2 | 4494108 | 4502574 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp5xl_n1re/f1.bed) resultresultresultresultresultresultresultresultresultresult chr2 503567 505146 - 1 chr2 4494108 4502574 - 1 bedtools_df Chromosome Start End Strand Count 0 chr2 503567 505146 - 1 1 chr2 4494108 4502574 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3704 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp1ck0u2i6/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 3704 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 3704 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4565 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpoiibc31f/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 4565 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 4565 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5887323 | 5890724 | a | 0 | - | | chr1 | 5603099 | 5608206 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpygev8_tp/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5603099 5608206 - 1 chr1 5887323 5890724 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 5603099 5608206 - 1 1 chr1 5887323 5890724 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6819550 | 6824364 | a | 0 | + | | chr17 | 6819550 | 6828013 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmphmcmlcjv/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6819550 6824364 + 1 chr17 6819550 6828013 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 6819550 6824364 + 1 1 chr17 6819550 6828013 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8153549 | 8161084 | a | 0 | + | | chr14 | 4884184 | 4888788 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpgk5jfca5/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8153549 8161084 + 1 chr14 4884184 4888788 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 8153549 8161084 + 1 1 chr14 4884184 4888788 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2186 | a | 0 | + | | chr1 | 238595 | 247323 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpg3yw3vaz/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2186 + 1 chr1 238595 247323 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2186 + 1 1 chr1 238595 247323 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 9064 | a | 0 | + | | chr1 | 1 | 9064 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp_3pcq5jy/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 9064 + 2 bedtools_df Chromosome Start End Strand Count 0 chr1 1 9064 + 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8157238 | 8159901 | a | 0 | + | | chr2 | 3425561 | 3428505 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp95l6y143/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8157238 8159901 + 1 chr2 3425561 3428505 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 8157238 8159901 + 1 1 chr2 3425561 3428505 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 8079 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpeerhcol1/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 8079 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 8079 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1993992 | 1993994 | a | 0 | + | | chr20 | 487219 | 490892 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp3nfcx5zl/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1993992 1993994 + 1 chr20 487219 490892 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1993992 1993994 + 1 1 chr20 487219 490892 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9082444 | 9085438 | a | 0 | - | | chr21 | 1728975 | 1738059 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp686ah1hg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9082444 9085438 - 1 chr21 1728975 1738059 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 9082444 9085438 - 1 1 chr21 1728975 1738059 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7690490 | 7693848 | a | 0 | + | | chr5 | 9723648 | 9732889 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmplsd2_zhq/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7690490 7693848 + 1 chr5 9723648 9732889 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 7690490 7693848 + 1 1 chr5 9723648 9732889 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1561291 | 1563965 | a | 0 | + | | chr1 | 5961186 | 5970505 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp0tt8mc0h/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1561291 1563965 + 1 chr1 5961186 5970505 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1561291 1563965 + 1 1 chr1 5961186 5970505 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 1 | 2169 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp09oa8spl/f1.bed) resultresultresultresultresultresultresultresultresultresult chr2 1 2169 + 1 bedtools_df Chromosome Start End Strand Count 0 chr2 1 2169 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2635913 | 2638562 | a | 0 | - | | chr1 | 4435585 | 4439532 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmphq4qr7ol/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2635913 2638562 - 1 chr1 4435585 4439532 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 2635913 2638562 - 1 1 chr1 4435585 4439532 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp58x2dy58/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 __________ test_three_in_a_row[strandedness_chain425-method_chain425] __________ [gw3] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('intersect', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 106 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain418-method_chain418] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 235, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'subtract'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | - | | | chr1 | 2120375 | 2120376 | a | 0 | - | | | chr1 | 1 | 2 | a | 0 | - | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 | (and 27 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZHR2z/jG6Jxrs5OBwREIGYEEI6Mjo7NC1HYgC4KAfIgsTATEAEMGAJBmCec=') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 381, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('nearest', 'subtract'), | gr=Empty PyRanges, | gr2=Empty PyRanges, # or any other generated value | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:15 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:369 | (and 24 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain416-method_chain416] __________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('nearest', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOMGBEiTGARkBQYMgAAWa4EHg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +13 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7023685 | 7023686 | a | 0 | ... | | chr1 | 7023685 | 7023686 | a | 0 | ... | | chr1 | 7023685 | 7023686 | a | 0 | ... | | chr1 | 7023685 | 7023686 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 18 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 13 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance, ... (+ 6 more.) ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') _____________________________ test_cluster[False] ______________________________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 strand = False @pytest.mark.bedtools > @pytest.mark.parametrize("strand", [True, False]) tests/test_unary.py:96: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:132: in test_cluster result = gr.cluster(strand=strand) pyranges/pyranges.py:1070: in cluster df = pyrange_apply_single(_cluster, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/cluster.py:14: in _cluster ids = annotate_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_cluster( E strand=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) sorted_nearest/src/annotate_clusters.pyx:15: Exception ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpwdx6beld/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9439422 | 9444745 | a | 0 | + | | chr1 | 2231654 | 2241653 | a | 0 | + | | chr1 | 8165767 | 8167533 | a | 0 | + | | chr6 | 3092527 | 3093932 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr16 | 7394535 | 7402326 | a | 0 | + | | chr17 | 3409820 | 3416518 | a | 0 | + | | chr20 | 5568439 | 5575887 | a | 0 | + | | chr21 | 5900692 | 5900694 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 9 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp05afhh9n/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2231654 2241653 a 0 + 1 1 chr1 8165767 8167533 a 0 + 2 2 chr1 9439422 9444745 a 0 + 3 3 chr10 5906546 5914463 a 0 + 4 4 chr16 7394535 7402326 a 0 + 5 5 chr17 3409820 3416518 a 0 + 6 6 chr20 5568439 5575887 a 0 + 7 7 chr21 5900692 5900694 a 0 + 8 8 chr6 3092527 3093932 a 0 + 9 9 chr7 8141124 8147000 a 0 - 10 10 chr8 4947309 4947506 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9439422 | 9444745 | a | 0 | + | | chr1 | 2231654 | 2241653 | a | 0 | + | | chr1 | 8165767 | 8167533 | a | 0 | + | | chr6 | 3092527 | 3093932 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr16 | 7394535 | 7402326 | a | 0 | + | | chr17 | 3409820 | 3416518 | a | 0 | + | | chr20 | 5568439 | 5575887 | a | 0 | + | | chr21 | 5900692 | 5900694 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 9 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9439422 | 9444745 | a | 0 | + | | chr1 | 2231654 | 2241653 | a | 0 | + | | chr1 | 8165767 | 8167533 | a | 0 | + | | chr6 | 3092527 | 3093932 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr16 | 7394535 | 7402326 | a | 0 | + | | chr17 | 3409820 | 3416518 | a | 0 | + | | chr20 | 5568439 | 5575887 | a | 0 | + | | chr21 | 5900692 | 5900694 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 9 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp_iigj3aa/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2231654 2241653 a 0 + 1 1 chr1 8165767 8167533 a 0 + 2 2 chr1 9439422 9444745 a 0 + 3 3 chr10 5906546 5914463 a 0 + 4 4 chr16 7394535 7402326 a 0 + 5 5 chr17 3409820 3416518 a 0 + 6 6 chr20 5568439 5575887 a 0 + 7 7 chr21 5900692 5900694 a 0 + 8 8 chr6 3092527 3093932 a 0 + 9 9 chr7 8141124 8147000 a 0 + 10 10 chr8 4947309 4947506 a 0 + 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9439422 | 9444745 | a | 0 | + | | chr1 | 2231654 | 2241653 | a | 0 | + | | chr1 | 8165767 | 8167533 | a | 0 | + | | chr6 | 3092527 | 3093932 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr16 | 7394535 | 7402326 | a | 0 | + | | chr17 | 3409820 | 3416518 | a | 0 | + | | chr20 | 5568439 | 5575887 | a | 0 | + | | chr21 | 5900692 | 5900694 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 9 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr6 | 1 | 21 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 1 | 21 | a | 0 | + | | chr16 | 1 | 21 | a | 0 | + | | chr17 | 1 | 21 | a | 0 | + | | chr20 | 1 | 21 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpahh9xk0_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 21 a 0 + 1 1 chr1 1 21 a 0 + 1 2 chr1 1 21 a 0 + 1 3 chr10 1 21 a 0 + 2 4 chr16 1 21 a 0 + 3 5 chr17 1 21 a 0 + 4 6 chr20 1 21 a 0 + 5 7 chr6 1 21 a 0 + 6 8 chr7 1 21 a 0 + 7 9 chr8 1 21 a 0 + 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr6 | 1 | 21 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 1 | 21 | a | 0 | + | | chr16 | 1 | 21 | a | 0 | + | | chr17 | 1 | 21 | a | 0 | + | | chr20 | 1 | 21 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 1 | 21 | a | 0 | + | | chr16 | 1 | 21 | a | 0 | + | | chr17 | 1 | 21 | a | 0 | + | | chr20 | 1 | 21 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpii73s__f/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 21 a 0 + 1 1 chr1 1 21 a 0 + 1 2 chr1 1 21 a 0 + 1 3 chr1 1 21 a 0 + 1 4 chr10 1 21 a 0 + 2 5 chr16 1 21 a 0 + 3 6 chr17 1 21 a 0 + 4 7 chr20 1 21 a 0 + 5 8 chr6 1 21 a 0 + 6 9 chr8 1 21 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr10 | 1 | 21 | a | 0 | + | | chr16 | 1 | 21 | a | 0 | + | | chr17 | 1 | 21 | a | 0 | + | | chr20 | 1 | 21 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr8 | 1 | 21 | a | 0 | + | | chr10 | 1 | 21 | a | 0 | + | | chr17 | 1 | 21 | a | 0 | + | | chr20 | 1 | 21 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmprclsk7jm/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 21 a 0 + 1 1 chr1 1 21 a 0 + 1 2 chr1 1 21 a 0 + 1 3 chr1 1 21 a 0 + 1 4 chr10 1 21 a 0 + 2 5 chr17 1 21 a 0 + 3 6 chr20 1 21 a 0 + 4 7 chr6 1 21 a 0 + 5 8 chr6 1 21 a 0 + 5 9 chr8 1 21 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr8 | 1 | 21 | a | 0 | + | | chr10 | 1 | 21 | a | 0 | + | | chr17 | 1 | 21 | a | 0 | + | | chr20 | 1 | 21 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr8 | 1 | 21 | a | 0 | + | | chr10 | 1 | 21 | a | 0 | + | | chr17 | 1 | 21 | a | 0 | + | | chr20 | 1 | 21 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpfxe38iwb/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 21 a 0 + 1 1 chr1 1 21 a 0 + 1 2 chr1 1 21 a 0 + 1 3 chr1 1 21 a 0 + 1 4 chr10 1 21 a 0 + 2 5 chr17 1 21 a 0 + 3 6 chr20 1 21 a 0 + 4 7 chr6 1 21 a 0 + 5 8 chr6 1 21 a 0 + 5 9 chr8 1 21 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr8 | 1 | 21 | a | 0 | + | | chr10 | 1 | 21 | a | 0 | + | | chr17 | 1 | 21 | a | 0 | + | | chr20 | 1 | 21 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 1 | 21 | a | 0 | + | | chr6 | 1 | 21 | a | 0 | + | | chr10 | 1 | 21 | a | 0 | + | | chr17 | 1 | 21 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpymrh9m0v/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 21 a 0 + 1 1 chr1 1 21 a 0 + 1 2 chr1 1 21 a 0 + 1 3 chr1 1 21 a 0 + 1 4 chr1 1 21 a 0 + 1 5 chr10 1 21 a 0 + 2 6 chr17 1 21 a 0 + 3 7 chr20 1 21 a 0 + 4 8 chr6 1 21 a 0 + 5 9 chr6 1 21 a 0 + 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | chr1 | 1 | 21 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr6 | 1 | 21 | a | 0 | + | | chr6 | 1 | 21 | a | 0 | + | | chr10 | 1 | 21 | a | 0 | + | | chr17 | 1 | 21 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5940384 | 5947969 | a | 0 | + | | chr1 | 9826866 | 9827775 | a | 0 | + | | chr1 | 9474960 | 9482918 | a | 0 | + | | chr1 | 1938776 | 1948643 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 3172823 | 3181058 | a | 0 | - | | chr1 | 8513032 | 8521126 | a | 0 | - | | chr1 | 9826866 | 9834019 | a | 0 | - | | chr1 | 4145545 | 4154344 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpk5lx76k8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1938776 1948643 a 0 + 1 1 chr1 3172823 3181058 a 0 - 2 2 chr1 4145545 4154344 a 0 - 3 3 chr1 5940384 5947969 a 0 + 4 4 chr1 8513032 8521126 a 0 - 5 5 chr1 9474960 9482918 a 0 + 6 6 chr1 9826866 9827775 a 0 + 7 7 chr1 9826866 9834019 a 0 - 7 8 chr11 5242512 5249138 a 0 - 8 9 chr14 8603368 8604743 a 0 + 9 10 chrY 9328808 9337607 a 0 - 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5940384 | 5947969 | a | 0 | + | | chr1 | 9826866 | 9827775 | a | 0 | + | | chr1 | 9474960 | 9482918 | a | 0 | + | | chr1 | 1938776 | 1948643 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 3172823 | 3181058 | a | 0 | - | | chr1 | 8513032 | 8521126 | a | 0 | - | | chr1 | 9826866 | 9834019 | a | 0 | - | | chr1 | 4145545 | 4154344 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5940384 | 5947969 | a | 0 | + | | chr1 | 9826866 | 9827775 | a | 0 | + | | chr1 | 9474960 | 9482918 | a | 0 | + | | chr1 | 1938776 | 1948643 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 3172823 | 3181058 | a | 0 | - | | chr1 | 8513032 | 8521126 | a | 0 | - | | chr1 | 9826866 | 9834019 | a | 0 | - | | chr1 | 4145545 | 4154344 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp5xz1ezzq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1938776 1948643 a 0 + 1 1 chr1 3172823 3181058 a 0 - 2 2 chr1 4145545 4154344 a 0 - 3 3 chr1 5940384 5947969 a 0 + 4 4 chr1 8513032 8521126 a 0 - 5 5 chr1 9474960 9482918 a 0 + 6 6 chr1 9826866 9827775 a 0 + 7 7 chr1 9826866 9834019 a 0 - 7 8 chr14 5242512 5249138 a 0 - 8 9 chr14 8603368 8604743 a 0 + 9 10 chrY 9328808 9337607 a 0 - 10 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5940384 | 5947969 | a | 0 | + | | chr1 | 9826866 | 9827775 | a | 0 | + | | chr1 | 9474960 | 9482918 | a | 0 | + | | chr1 | 1938776 | 1948643 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr1 | 3172823 | 3181058 | a | 0 | - | | chr1 | 8513032 | 8521126 | a | 0 | - | | chr1 | 9826866 | 9834019 | a | 0 | - | | chr1 | 4145545 | 4154344 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpntb3uwur/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpf0mf6y0s/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp4d_q6yss/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3816692 | 3820507 | a | 0 | + | | chr1 | 9724672 | 9724673 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpaw22vtek/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3816692 3820507 a 0 + 1 1 chr1 9724672 9724673 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3816692 | 3820507 | a | 0 | + | | chr1 | 9724672 | 9724673 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4447 | a | 0 | + | | chr1 | 1 | 4447 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmppjzq4h6o/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 4447 a 0 + 1 1 chr1 1 4447 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4447 | a | 0 | + | | chr1 | 1 | 4447 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4448900 | 4452600 | a | 0 | + | | chr1 | 1795431 | 1797601 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpv2q1__7i/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1795431 1797601 a 0 - 1 1 chr1 4448900 4452600 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4448900 | 4452600 | a | 0 | + | | chr1 | 1795431 | 1797601 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1575051 | 1583184 | a | 0 | - | | chr8 | 9617058 | 9622250 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp6ew49ekx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1575051 1583184 a 0 - 1 1 chr8 9617058 9622250 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1575051 | 1583184 | a | 0 | - | | chr8 | 9617058 | 9622250 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7495869 | 7503334 | a | 0 | + | | chr1 | 5181124 | 5187754 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpyjyh8b4b/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5181124 5187754 a 0 - 1 1 chr1 7495869 7503334 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7495869 | 7503334 | a | 0 | + | | chr1 | 5181124 | 5187754 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 8179 | a | 0 | - | | chr1 | 1 | 8179 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmph_z3io2e/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 8179 a 0 - 1 1 chr1 1 8179 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 8179 | a | 0 | - | | chr1 | 1 | 8179 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1768135 | 1777811 | a | 0 | + | | chr21 | 6404729 | 6405801 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpvcf0abq3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1768135 1777811 a 0 + 1 1 chr21 6404729 6405801 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1768135 | 1777811 | a | 0 | + | | chr21 | 6404729 | 6405801 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4808 | a | 0 | - | | chr1 | 1 | 4808 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp1c9zkcpg/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 4808 a 0 - 1 1 chr1 1 4808 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4808 | a | 0 | - | | chr1 | 1 | 4808 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8873279 | 8877665 | a | 0 | - | | chr6 | 8801843 | 8809796 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpl9_yd2zm/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8873279 8877665 a 0 - 1 1 chr6 8801843 8809796 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8873279 | 8877665 | a | 0 | - | | chr6 | 8801843 | 8809796 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 533304 | 533632 | a | 0 | + | | chrX | 2614591 | 2621376 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp12rp2yw9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 533304 533632 a 0 + 1 1 chrX 2614591 2621376 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 533304 | 533632 | a | 0 | + | | chrX | 2614591 | 2621376 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5738468 | 5745279 | a | 0 | + | | chr1 | 3361734 | 3363296 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpbpa9s7lv/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3361734 3363296 a 0 - 1 1 chr1 5738468 5745279 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5738468 | 5745279 | a | 0 | + | | chr1 | 3361734 | 3363296 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 5645 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpsx3z57oy/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 5645 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 5645 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4560615 | 4568536 | a | 0 | + | | chr13 | 5343067 | 5348832 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpa07i98dn/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4560615 4568536 a 0 + 1 1 chr13 5343067 5348832 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4560615 | 4568536 | a | 0 | + | | chr13 | 5343067 | 5348832 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 7834 | a | 0 | + | | chr1 | 6536577 | 6545076 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpueysc2d3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2 7834 a 0 + 1 1 chr1 6536577 6545076 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 7834 | a | 0 | + | | chr1 | 6536577 | 6545076 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8657936 | 8658662 | a | 0 | - | | chr12 | 10000000 | 10009368 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp4pgj6dr7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8657936 8658662 a 0 - 1 1 chr12 10000000 10009368 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8657936 | 8658662 | a | 0 | - | | chr12 | 10000000 | 10009368 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 432 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpjusn60vm/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 432 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 432 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2509631 | 2517915 | a | 0 | + | | chr3 | 2509631 | 2514720 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp4g9hdlkp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2509631 2517915 a 0 + 1 1 chr3 2509631 2514720 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2509631 | 2517915 | a | 0 | + | | chr3 | 2509631 | 2514720 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4957099 | 4965034 | a | 0 | - | | chr1 | 4455468 | 4463403 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpxq0vomhf/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4455468 4463403 a 0 - 1 1 chr1 4957099 4965034 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4957099 | 4965034 | a | 0 | - | | chr1 | 4455468 | 4463403 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 754368 | 762619 | a | 0 | - | | chr1 | 8989691 | 8996416 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp2qgf28tl/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 754368 762619 a 0 - 1 1 chr1 8989691 8996416 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 754368 | 762619 | a | 0 | - | | chr1 | 8989691 | 8996416 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9335742 | 9338849 | a | 0 | - | | chr16 | 4440946 | 4441775 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpvrbzs_a5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9335742 9338849 a 0 - 1 1 chr16 4440946 4441775 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9335742 | 9338849 | a | 0 | - | | chr16 | 4440946 | 4441775 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8475663 | 8480552 | a | 0 | - | | chr1 | 8441642 | 8449560 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpy71ft2b4/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8441642 8449560 a 0 - 1 1 chr1 8475663 8480552 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8475663 | 8480552 | a | 0 | - | | chr1 | 8441642 | 8449560 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3850870 | 3854348 | a | 0 | + | | chr1 | 3425483 | 3432921 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp4a49dm61/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3425483 3432921 a 0 - 1 1 chr1 3850870 3854348 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3850870 | 3854348 | a | 0 | + | | chr1 | 3425483 | 3432921 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3140 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpk0s96l9x/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 3140 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3140 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 130688 | 140605 | a | 0 | - | | chr19 | 9159521 | 9164126 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmphlpqv3mq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 130688 140605 a 0 - 1 1 chr19 9159521 9164126 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 130688 | 140605 | a | 0 | - | | chr19 | 9159521 | 9164126 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 6681 | a | 0 | + | | chr1 | 1 | 6681 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp1nhkegre/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 6681 a 0 + 1 1 chr1 1 6681 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 6681 | a | 0 | + | | chr1 | 1 | 6681 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9254624 | 9260121 | a | 0 | + | | chr1 | 1323974 | 1331815 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp7w0bytiq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1323974 1331815 a 0 + 1 1 chr1 9254624 9260121 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9254624 | 9260121 | a | 0 | + | | chr1 | 1323974 | 1331815 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1759371 | 1764139 | a | 0 | - | | chrY | 1759371 | 1759372 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp5tda4uhk/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1759371 1764139 a 0 - 1 1 chrY 1759371 1759372 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1759371 | 1764139 | a | 0 | - | | chrY | 1759371 | 1759372 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9473160 | 9474840 | a | 0 | + | | chr2 | 6101653 | 6106619 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpn9fgn740/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9473160 9474840 a 0 + 1 1 chr2 6101653 6106619 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9473160 | 9474840 | a | 0 | + | | chr2 | 6101653 | 6106619 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8400409 | 8409067 | a | 0 | + | | chr1 | 7749055 | 7753558 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpu0nrn9tu/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7749055 7753558 a 0 - 1 1 chr1 8400409 8409067 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8400409 | 8409067 | a | 0 | + | | chr1 | 7749055 | 7753558 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9553765 | 9560525 | a | 0 | - | | chr19 | 1907888 | 1915428 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpnx_8i4_g/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9553765 9560525 a 0 - 1 1 chr19 1907888 1915428 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9553765 | 9560525 | a | 0 | - | | chr19 | 1907888 | 1915428 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5058488 | 5066129 | a | 0 | - | | chrY | 7143038 | 7149215 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpynk0obha/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5058488 5066129 a 0 - 1 1 chrY 7143038 7149215 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5058488 | 5066129 | a | 0 | - | | chrY | 7143038 | 7149215 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1421096 | 1426524 | a | 0 | - | | chr19 | 1111885 | 1115355 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpx_3kjlgs/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1421096 1426524 a 0 - 1 1 chr19 1111885 1115355 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1421096 | 1426524 | a | 0 | - | | chr19 | 1111885 | 1115355 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3646932 | 3655615 | a | 0 | - | | chr17 | 2281056 | 2289145 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpml13tett/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3646932 3655615 a 0 - 1 1 chr17 2281056 2289145 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3646932 | 3655615 | a | 0 | - | | chr17 | 2281056 | 2289145 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5209859 | 5211114 | a | 0 | + | | chr1 | 6595524 | 6598497 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpvvb3ifdl/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5209859 5211114 a 0 + 1 1 chr1 6595524 6598497 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5209859 | 5211114 | a | 0 | + | | chr1 | 6595524 | 6598497 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3747416 | 3751681 | a | 0 | + | | chr1 | 3747416 | 3756048 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp_4ac8my_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3747416 3751681 a 0 + 1 1 chr1 3747416 3756048 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3747416 | 3751681 | a | 0 | + | | chr1 | 3747416 | 3756048 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5049583 | 5058491 | a | 0 | + | | chr1 | 9337551 | 9346450 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp_aiamtgg/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5049583 5058491 a 0 + 1 1 chr1 9337551 9346450 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5049583 | 5058491 | a | 0 | + | | chr1 | 9337551 | 9346450 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3393876 | 3395114 | a | 0 | + | | chr1 | 7449607 | 7456801 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp3gfrqjba/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3393876 3395114 a 0 + 1 1 chr1 7449607 7456801 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3393876 | 3395114 | a | 0 | + | | chr1 | 7449607 | 7456801 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4957 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpox47jx2_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 4957 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4957 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1622191 | 1631960 | a | 0 | - | | chr1 | 7635862 | 7643946 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmphsewv1l9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1622191 1631960 a 0 - 1 1 chr1 7635862 7643946 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1622191 | 1631960 | a | 0 | - | | chr1 | 7635862 | 7643946 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 905 | a | 0 | + | | chr1 | 1 | 905 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpy0v8hema/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 905 a 0 + 1 1 chr1 1 905 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 905 | a | 0 | + | | chr1 | 1 | 905 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4499944 | 4505521 | a | 0 | + | | chr1 | 2208530 | 2211482 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpmiv1wobo/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2208530 2211482 a 0 - 1 1 chr1 4499944 4505521 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4499944 | 4505521 | a | 0 | + | | chr1 | 2208530 | 2211482 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1488241 | 1494475 | a | 0 | - | | chr1 | 10000000 | 10001837 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpo6faneme/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1488241 1494475 a 0 - 1 1 chr1 10000000 10001837 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1488241 | 1494475 | a | 0 | - | | chr1 | 10000000 | 10001837 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 8875 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpqz8qjq1w/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 8875 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 8875 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1867778 | 1873750 | a | 0 | - | | chr1 | 1970290 | 1972567 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpc0yetb46/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1867778 1873750 a 0 - 1 1 chr1 1970290 1972567 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1867778 | 1873750 | a | 0 | - | | chr1 | 1970290 | 1972567 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4301 | a | 0 | - | | chr1 | 1 | 4301 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpeudryzaz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 4301 a 0 - 1 1 chr1 1 4301 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4301 | a | 0 | - | | chr1 | 1 | 4301 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7108222 | 7114756 | a | 0 | + | | chr20 | 1158253 | 1160784 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp8oequ_i1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7108222 7114756 a 0 + 1 1 chr20 1158253 1160784 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7108222 | 7114756 | a | 0 | + | | chr20 | 1158253 | 1160784 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3314 | a | 0 | - | | chr1 | 1 | 3314 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp7mwtd91s/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 3314 a 0 - 1 1 chr1 1 3314 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3314 | a | 0 | - | | chr1 | 1 | 3314 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5906295 | 5913115 | a | 0 | + | | chr1 | 9423383 | 9429356 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpjxld3vh7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5906295 5913115 a 0 + 1 1 chr1 9423383 9429356 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5906295 | 5913115 | a | 0 | + | | chr1 | 9423383 | 9429356 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 5344 | a | 0 | + | | chr1 | 1 | 5344 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp67zefsdz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 5344 a 0 + 1 1 chr1 1 5344 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 5344 | a | 0 | + | | chr1 | 1 | 5344 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5354049 | 5360105 | a | 0 | - | | chr22 | 6898490 | 6903595 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp5ps4uplz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5354049 5360105 a 0 - 1 1 chr22 6898490 6903595 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5354049 | 5360105 | a | 0 | - | | chr22 | 6898490 | 6903595 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 6837 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpx69msgmz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 6837 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 6837 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 1108 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmposovsadu/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 1108 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 1108 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9886020 | 9891177 | a | 0 | - | | chr1 | 727441 | 733461 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp41y3ii12/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 727441 733461 a 0 - 1 1 chr1 9886020 9891177 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9886020 | 9891177 | a | 0 | - | | chr1 | 727441 | 733461 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9083373 | 9088602 | a | 0 | + | | chrM | 7968061 | 7973782 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpwbrn6iqr/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9083373 9088602 a 0 + 1 1 chrM 7968061 7973782 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9083373 | 9088602 | a | 0 | + | | chrM | 7968061 | 7973782 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 1175 | a | 0 | - | | chr1 | 1 | 1175 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpsxu6wozo/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 1175 a 0 - 1 1 chr1 1 1175 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 1175 | a | 0 | - | | chr1 | 1 | 1175 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3920213 | 3921125 | a | 0 | + | | chr1 | 4696035 | 4702053 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp3nn4nkx8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3920213 3921125 a 0 + 1 1 chr1 4696035 4702053 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3920213 | 3921125 | a | 0 | + | | chr1 | 4696035 | 4702053 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3202683 | 3211071 | a | 0 | + | | chr1 | 2124810 | 2125698 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmptyyr5478/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2124810 2125698 a 0 + 1 1 chr1 3202683 3211071 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3202683 | 3211071 | a | 0 | + | | chr1 | 2124810 | 2125698 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4545086 | 4552535 | a | 0 | + | | chr15 | 9753530 | 9760979 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpaeedv7oi/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4545086 4552535 a 0 + 1 1 chr15 9753530 9760979 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4545086 | 4552535 | a | 0 | + | | chr15 | 9753530 | 9760979 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2622560 | 2623589 | a | 0 | - | | chr1 | 7103970 | 7110170 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpwdn_8c_g/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2622560 2623589 a 0 - 1 1 chr1 7103970 7110170 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2622560 | 2623589 | a | 0 | - | | chr1 | 7103970 | 7110170 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4059666 | 4066894 | a | 0 | + | | chr1 | 2398129 | 2405357 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp2oxto32o/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2398129 2405357 a 0 - 1 1 chr1 4059666 4066894 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4059666 | 4066894 | a | 0 | + | | chr1 | 2398129 | 2405357 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3468729 | 3474688 | a | 0 | - | | chr13 | 3468729 | 3476706 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpkr5azac5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3468729 3474688 a 0 - 1 1 chr13 3468729 3476706 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3468729 | 3474688 | a | 0 | - | | chr13 | 3468729 | 3476706 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2950 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpzrxsxc0n/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2950 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2950 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4411 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpu941ojbe/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 4411 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4411 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4714700 | 4720970 | a | 0 | + | | chr1 | 543195 | 550917 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmphyj_y20w/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 543195 550917 a 0 - 1 1 chr1 4714700 4720970 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4714700 | 4720970 | a | 0 | + | | chr1 | 543195 | 550917 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 7348 | a | 0 | + | | chr1 | 1 | 7348 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpjlrmozs8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 7348 a 0 + 1 1 chr1 1 7348 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 7348 | a | 0 | + | | chr1 | 1 | 7348 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9982103 | 9986573 | a | 0 | + | | chr1 | 591417 | 594480 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpg89kvukc/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 591417 594480 a 0 + 1 1 chr1 9982103 9986573 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9982103 | 9986573 | a | 0 | + | | chr1 | 591417 | 594480 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2426447 | 2426449 | a | 0 | - | | chr8 | 2426447 | 2436447 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp_x8u3clk/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2426447 2426449 a 0 - 1 1 chr8 2426447 2436447 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2426447 | 2426449 | a | 0 | - | | chr8 | 2426447 | 2436447 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6342446 | 6342847 | a | 0 | + | | chr9 | 4074842 | 4082475 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp1p6f7e6i/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6342446 6342847 a 0 + 1 1 chr9 4074842 4082475 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6342446 | 6342847 | a | 0 | + | | chr9 | 4074842 | 4082475 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1604329 | 1605384 | a | 0 | + | | chr1 | 8429567 | 8437647 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmplez0p450/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1604329 1605384 a 0 + 1 1 chr1 8429567 8437647 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1604329 | 1605384 | a | 0 | + | | chr1 | 8429567 | 8437647 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 345 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpl62pdn5e/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 345 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 345 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1290764 | 1298222 | a | 0 | - | | chr22 | 5079227 | 5084866 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpt9xdlrx1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1290764 1298222 a 0 - 1 1 chr22 5079227 5084866 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1290764 | 1298222 | a | 0 | - | | chr22 | 5079227 | 5084866 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2510953 | 2519779 | a | 0 | + | | chr10 | 2801890 | 2805363 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpf8s9c9ip/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2510953 2519779 a 0 + 1 1 chr10 2801890 2805363 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2510953 | 2519779 | a | 0 | + | | chr10 | 2801890 | 2805363 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6981571 | 6983620 | a | 0 | - | | chr21 | 2822448 | 2823994 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpbohcdwe_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6981571 6983620 a 0 - 1 1 chr21 2822448 2823994 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6981571 | 6983620 | a | 0 | - | | chr21 | 2822448 | 2823994 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9114362 | 9123095 | a | 0 | + | | chr1 | 6101174 | 6109203 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp5ru3m_qy/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6101174 6109203 a 0 + 1 1 chr1 9114362 9123095 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9114362 | 9123095 | a | 0 | + | | chr1 | 6101174 | 6109203 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5412056 | 5417602 | a | 0 | - | | chr1 | 4772515 | 4772517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpykvf74z7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4772515 4772517 a 0 - 1 1 chr1 5412056 5417602 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5412056 | 5417602 | a | 0 | - | | chr1 | 4772515 | 4772517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 6949 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpm3hykv59/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 6949 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 6949 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5135981 | 5144126 | a | 0 | + | | chrM | 5631508 | 5635871 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpcyrgsaej/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5135981 5144126 a 0 + 1 1 chrM 5631508 5635871 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5135981 | 5144126 | a | 0 | + | | chrM | 5631508 | 5635871 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmphkbkl65v/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3340333 | 3343480 | a | 0 | + | | chr1 | 5547190 | 5557189 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpm2co9vwc/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3340333 3343480 a 0 + 1 1 chr1 5547190 5557189 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3340333 | 3343480 | a | 0 | + | | chr1 | 5547190 | 5557189 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5919299 | 5922759 | a | 0 | + | | chr1 | 4919993 | 4921253 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpu528hahk/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4919993 4921253 a 0 - 1 1 chr1 5919299 5922759 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5919299 | 5922759 | a | 0 | + | | chr1 | 4919993 | 4921253 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4420 | a | 0 | - | | chr1 | 1 | 4420 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp4wfw6it8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 4420 a 0 - 1 1 chr1 1 4420 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4420 | a | 0 | - | | chr1 | 1 | 4420 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3186 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpqhzrm3w2/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 3186 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3186 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 1674 | a | 0 | - | | chr1 | 1 | 1674 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpfok6julz/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 1674 a 0 - 1 1 chr1 1 1674 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 1674 | a | 0 | - | | chr1 | 1 | 1674 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2319685 | 2323164 | a | 0 | + | | chr14 | 9229621 | 9235136 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpz1lb3cdc/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2319685 2323164 a 0 + 1 1 chr14 9229621 9235136 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2319685 | 2323164 | a | 0 | + | | chr14 | 9229621 | 9235136 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 8079 | a | 0 | + | | chr1 | 5649858 | 5656377 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpnlm12atl/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 8079 a 0 + 1 1 chr1 5649858 5656377 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 8079 | a | 0 | + | | chr1 | 5649858 | 5656377 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10005438 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp9qnlceu9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 10000000 10005438 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10005438 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5909424 | 5917853 | a | 0 | + | | chr1 | 2683011 | 2685502 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp6usrf2h0/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2683011 2685502 a 0 - 1 1 chr1 5909424 5917853 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5909424 | 5917853 | a | 0 | + | | chr1 | 2683011 | 2685502 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 8970 | a | 0 | + | | chr1 | 1 | 8970 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpo4wj6a6c/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 8970 a 0 + 1 1 chr1 1 8970 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 8970 | a | 0 | + | | chr1 | 1 | 8970 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4086243 | 4089067 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpkgpf1k59/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4086243 4089067 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4086243 | 4089067 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 968 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp5jsm_dd3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 968 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 968 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 5950 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp09zdagxn/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 5950 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 5950 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8778057 | 8780731 | a | 0 | - | | chr20 | 10000000 | 10002674 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp1vqb7c5o/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8778057 8780731 a 0 - 1 1 chr20 10000000 10002674 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8778057 | 8780731 | a | 0 | - | | chr20 | 10000000 | 10002674 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 10001 | a | 0 | + | | chr1 | 1 | 10001 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpp1bf1xju/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 10001 a 0 + 1 1 chr1 1 10001 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 10001 | a | 0 | + | | chr1 | 1 | 10001 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7788921 | 7794673 | a | 0 | - | | chr1 | 54871 | 60623 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp0v3fntm9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 54871 60623 a 0 - 1 1 chr1 7788921 7794673 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7788921 | 7794673 | a | 0 | - | | chr1 | 54871 | 60623 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 464 | a | 0 | - | | chr1 | 1 | 464 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpfyn7w4w6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 464 a 0 - 1 1 chr1 1 464 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 464 | a | 0 | - | | chr1 | 1 | 464 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4003870 | 4008728 | a | 0 | + | | chr9 | 6687281 | 6690423 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmprubj2xa2/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4003870 4008728 a 0 + 1 1 chr9 6687281 6690423 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4003870 | 4008728 | a | 0 | + | | chr9 | 6687281 | 6690423 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 738377 | 741070 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpyhcpbo0x/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 738377 741070 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 738377 | 741070 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 809564 | 815530 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpoo0voa__/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 809564 815530 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 809564 | 815530 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2235260 | 2238005 | a | 0 | + | | chr1 | 2235260 | 2245260 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpz3jubvva/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2235260 2238005 a 0 + 1 1 chr1 2235260 2245260 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2235260 | 2238005 | a | 0 | + | | chr1 | 2235260 | 2245260 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5122255 | 5130887 | a | 0 | - | | chrX | 9954346 | 9962978 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpflpq0nyv/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5122255 5130887 a 0 - 1 1 chrX 9954346 9962978 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5122255 | 5130887 | a | 0 | - | | chrX | 9954346 | 9962978 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpfzd_rcra/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. __________ test_three_in_a_row[strandedness_chain439-method_chain439] __________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('join', 'subtract'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:15 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:145 E (and 24 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ______________________________ test_merge[False] _______________________________ [gw1] linux -- Python 3.13.2 /usr/bin/python3.13 strand = False @pytest.mark.bedtools > @pytest.mark.parametrize("strand", [True, False]) tests/test_unary.py:31: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:75: in test_merge result = gr.merge(strand=strand, count=True) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_merge( E strand=False, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpetzkb4fa/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr8 | 1185798 | 1189771 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp_c3wd9sa/f1.bed) resultresultresultresultresultresultresultresultresultresult chr8 1185798 1189771 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr8 1185798 1189771 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1185798 | 1185799 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpq_rdz_iw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1185798 1185799 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1185798 1185799 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpovpy3fam/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpd5v7z6rw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 9711998 | 9714935 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpx3q5t3c8/f1.bed) resultresultresultresultresultresultresultresultresultresult chr10 9711998 9714935 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr10 9711998 9714935 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 2937 | 5874 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpg82em8ro/f1.bed) resultresultresultresultresultresultresultresultresultresult chr10 2937 5874 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr10 2937 5874 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 2937 | 5874 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpb1s28fxr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr10 2937 5874 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr10 2937 5874 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr10 | 2937 | 5874 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp707rnjvn/f1.bed) resultresultresultresultresultresultresultresultresultresult chr10 2937 5874 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr10 2937 5874 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2937 | 2938 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmppr_670cb/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2937 2938 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2937 2938 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpia67fs3l/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpfrhs05cc/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmplo005q46/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2015286 | 2017318 | a | 0 | + | | chr22 | 7218562 | 7222492 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpo8oxjr2l/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2015286 2017318 + 1 chr22 7218562 7222492 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2015286 2017318 1 1 chr22 7218562 7222492 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1126263 | 1129316 | a | 0 | + | | chr1 | 7699279 | 7701104 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp3p56owpw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1126263 1129316 + 1 chr1 7699279 7701104 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1126263 1129316 1 1 chr1 7699279 7701104 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9527391 | 9536050 | a | 0 | + | | chr5 | 7625079 | 7633738 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp4eaxwhzl/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9527391 9536050 + 1 chr5 7625079 7633738 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 9527391 9536050 1 1 chr5 7625079 7633738 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1718650 | 1725721 | a | 0 | - | | chr18 | 7842042 | 7849113 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp9s_4_0xb/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1718650 1725721 - 1 chr18 7842042 7849113 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1718650 1725721 1 1 chr18 7842042 7849113 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8619576 | 8619577 | a | 0 | + | | chrY | 2838424 | 2847546 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp6znlrjm_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8619576 8619577 + 1 chrY 2838424 2847546 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 8619576 8619577 1 1 chrY 2838424 2847546 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7308417 | 7310710 | a | 0 | + | | chr20 | 1594100 | 1600983 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp80z5hpl_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7308417 7310710 + 1 chr20 1594100 1600983 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 7308417 7310710 1 1 chr20 1594100 1600983 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6859819 | 6861202 | a | 0 | + | | chr1 | 5131354 | 5135946 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpev8ikn4e/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5131354 5135946 - 1 chr1 6859819 6861202 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5131354 5135946 1 1 chr1 6859819 6861202 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 975437 | 983733 | a | 0 | - | | chr9 | 3301162 | 3302566 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp3ad2ughl/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 975437 983733 - 1 chr9 3301162 3302566 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 975437 983733 1 1 chr9 3301162 3302566 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4716 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpyjwev8p0/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 4716 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 4716 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5633808 | 5641629 | a | 0 | + | | chr1 | 7258754 | 7261073 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpqzt6k0xf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5633808 5641629 + 1 chr1 7258754 7261073 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5633808 5641629 1 1 chr1 7258754 7261073 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3080 | a | 0 | + | | chr1 | 1 | 3080 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmprj66etig/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 3080 + 2 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 3080 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2916182 | 2922061 | a | 0 | + | | chr1 | 593381 | 594449 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpa5vishpw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 593381 594449 - 1 chr1 2916182 2922061 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 593381 594449 1 1 chr1 2916182 2922061 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4235305 | 4242495 | a | 0 | + | | chr1 | 5085088 | 5094030 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp2nvkukgg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4235305 4242495 + 1 chr1 5085088 5094030 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 4235305 4242495 1 1 chr1 5085088 5094030 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3880065 | 3886797 | a | 0 | - | | chr14 | 9527110 | 9528271 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpyn_t6cgf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3880065 3886797 - 1 chr14 9527110 9528271 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3880065 3886797 1 1 chr14 9527110 9528271 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 390637 | 391581 | a | 0 | + | | chr1 | 5097064 | 5100615 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpxvheeskb/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 390637 391581 + 1 chr1 5097064 5100615 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 390637 391581 1 1 chr1 5097064 5100615 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9129303 | 9132095 | a | 0 | + | | chr1 | 2406749 | 2410819 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpowxm40td/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2406749 2410819 - 1 chr1 9129303 9132095 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2406749 2410819 1 1 chr1 9129303 9132095 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2 | 5615 | a | 0 | - | | chr10 | 9865800 | 9865802 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpg5rdhxa4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2 5615 - 1 chr10 9865800 9865802 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2 5615 1 1 chr10 9865800 9865802 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9827537 | 9833730 | a | 0 | + | | chr7 | 241719 | 244947 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpfhoq63u4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9827537 9833730 + 1 chr7 241719 244947 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 9827537 9833730 1 1 chr7 241719 244947 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1003653 | 1003928 | a | 0 | - | | chr1 | 1003653 | 1006988 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmphtdzeaij/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1003653 1006988 - 2 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1003653 1006988 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9111929 | 9117403 | a | 0 | - | | chrM | 1768376 | 1774401 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmptk6i0u88/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9111929 9117403 - 1 chrM 1768376 1774401 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 9111929 9117403 1 1 chrM 1768376 1774401 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 909751 | 910899 | a | 0 | + | | chr15 | 8134689 | 8142194 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp1o7txveg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 909751 910899 + 1 chr15 8134689 8142194 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 909751 910899 1 1 chr15 8134689 8142194 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5730739 | 5739500 | a | 0 | + | | chr1 | 7721189 | 7722258 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp8hsm4ymb/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5730739 5739500 + 1 chr1 7721189 7722258 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5730739 5739500 1 1 chr1 7721189 7722258 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3462586 | 3466194 | a | 0 | + | | chr19 | 3462586 | 3462962 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpb_5tgz6o/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3462586 3466194 + 1 chr19 3462586 3462962 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3462586 3466194 1 1 chr19 3462586 3462962 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10008023 | a | 0 | + | | chr1 | 10000000 | 10007402 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpr7bnkt4h/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 10000000 10008023 + 2 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 10000000 10008023 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2347772 | 2349114 | a | 0 | + | | chr1 | 3703060 | 3710850 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpzp027q79/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2347772 2349114 + 1 chr1 3703060 3710850 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2347772 2349114 1 1 chr1 3703060 3710850 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2523528 | 2531086 | a | 0 | + | | chr1 | 9104455 | 9105190 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpkungfjcq/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2523528 2531086 + 1 chr1 9104455 9105190 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2523528 2531086 1 1 chr1 9104455 9105190 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 5628 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp8unsr56s/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 5628 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 5628 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1265163 | 1272694 | a | 0 | + | | chr1 | 617631 | 622962 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpam46_hgo/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 617631 622962 - 1 chr1 1265163 1272694 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 617631 622962 1 1 chr1 1265163 1272694 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6386802 | 6394727 | a | 0 | + | | chr1 | 6174037 | 6179671 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp1kdl4ddp/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6174037 6179671 + 1 chr1 6386802 6394727 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6174037 6179671 1 1 chr1 6386802 6394727 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7053235 | 7060514 | a | 0 | + | | chr1 | 467016 | 477016 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmprqngcf24/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 467016 477016 + 1 chr1 7053235 7060514 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 467016 477016 1 1 chr1 7053235 7060514 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1898568 | 1904591 | a | 0 | + | | chr7 | 7967425 | 7972036 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmprogn69p2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1898568 1904591 + 1 chr7 7967425 7972036 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1898568 1904591 1 1 chr7 7967425 7972036 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7045631 | 7051537 | a | 0 | - | | chr1 | 5725690 | 5726807 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp4stshmgp/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5725690 5726807 - 1 chr1 7045631 7051537 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5725690 5726807 1 1 chr1 7045631 7051537 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9924040 | 9931519 | a | 0 | + | | chr1 | 2982776 | 2986990 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpsm4_lcjc/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2982776 2986990 - 1 chr1 9924040 9931519 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2982776 2986990 1 1 chr1 9924040 9931519 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8337318 | 8341991 | a | 0 | - | | chrX | 4410506 | 4418850 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpfdfyuqbh/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8337318 8341991 - 1 chrX 4410506 4418850 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 8337318 8341991 1 1 chrX 4410506 4418850 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7517601 | 7524587 | a | 0 | - | | chr1 | 8959141 | 8959881 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpdeijlzqj/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7517601 7524587 - 1 chr1 8959141 8959881 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 7517601 7524587 1 1 chr1 8959141 8959881 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7935561 | 7939763 | a | 0 | + | | chr3 | 4338473 | 4342997 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpmcgg_fug/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7935561 7939763 + 1 chr3 4338473 4342997 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 7935561 7939763 1 1 chr3 4338473 4342997 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10008529 | a | 0 | + | | chr7 | 10000000 | 10009779 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpimw2hl17/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 10000000 10008529 + 1 chr7 10000000 10009779 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 10000000 10008529 1 1 chr7 10000000 10009779 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2800452 | 2801564 | a | 0 | + | | chr1 | 2843225 | 2849857 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpta4qegkx/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2800452 2801564 + 1 chr1 2843225 2849857 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2800452 2801564 1 1 chr1 2843225 2849857 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2636955 | 2637641 | a | 0 | - | | chr19 | 8689267 | 8689953 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpqh9hxptd/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2636955 2637641 - 1 chr19 8689267 8689953 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2636955 2637641 1 1 chr19 8689267 8689953 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3178808 | 3180945 | a | 0 | + | | chr14 | 7472278 | 7474415 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp9uxjswxm/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3178808 3180945 + 1 chr14 7472278 7474415 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3178808 3180945 1 1 chr14 7472278 7474415 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 186721 | 191511 | a | 0 | - | | chr7 | 6694817 | 6700706 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp082gywjm/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 186721 191511 - 1 chr7 6694817 6700706 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 186721 191511 1 1 chr7 6694817 6700706 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5097291 | 5101822 | a | 0 | + | | chr22 | 8045904 | 8055904 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmptmz7pa41/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5097291 5101822 + 1 chr22 8045904 8055904 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5097291 5101822 1 1 chr22 8045904 8055904 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3939 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp0em1qylu/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 3939 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 3939 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4732 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp0h9moos2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 4732 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 4732 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 170 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpou1s2cu8/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 170 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 170 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3473 | a | 0 | - | | chr1 | 1 | 3473 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpr6mj_37h/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 3473 - 2 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 3473 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3781824 | 3785689 | a | 0 | + | | chr11 | 5790304 | 5798904 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpm147qxun/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3781824 3785689 + 1 chr11 5790304 5798904 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3781824 3785689 1 1 chr11 5790304 5798904 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3621616 | 3626603 | a | 0 | - | | chr3 | 357125 | 361725 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp27gzhskm/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3621616 3626603 - 1 chr3 357125 361725 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3621616 3626603 1 1 chr3 357125 361725 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5859422 | 5865011 | a | 0 | - | | chr1 | 5859422 | 5862875 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp6xg6udwt/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5859422 5865011 - 2 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5859422 5865011 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8471759 | 8472694 | a | 0 | + | | chr1 | 5374043 | 5374899 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpm1f53cfm/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5374043 5374899 + 1 chr1 8471759 8472694 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5374043 5374899 1 1 chr1 8471759 8472694 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8063676 | 8067900 | a | 0 | - | | chr18 | 1019685 | 1021456 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpmkg5povy/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8063676 8067900 - 1 chr18 1019685 1021456 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 8063676 8067900 1 1 chr18 1019685 1021456 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5217487 | 5221834 | a | 0 | + | | chr3 | 193850 | 197294 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpokrz1to5/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5217487 5221834 + 1 chr3 193850 197294 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5217487 5221834 1 1 chr3 193850 197294 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 170151 | 172266 | a | 0 | - | | chr1 | 9411253 | 9420097 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpp3636d1l/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 170151 172266 - 1 chr1 9411253 9420097 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 170151 172266 1 1 chr1 9411253 9420097 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 7466 | a | 0 | + | | chr1 | 1 | 7466 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpfx_idqns/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 7466 + 2 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 7466 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 840903 | 841159 | a | 0 | + | | chr1 | 2594814 | 2598694 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp62i3cc9v/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 840903 841159 + 1 chr1 2594814 2598694 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 840903 841159 1 1 chr1 2594814 2598694 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 806 | a | 0 | - | | chr1 | 1 | 806 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpiyijg3rt/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 806 - 2 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 806 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6327098 | 6337097 | a | 0 | + | | chr3 | 5922559 | 5924473 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpvgxmuxyu/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6327098 6337097 + 1 chr3 5922559 5924473 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6327098 6337097 1 1 chr3 5922559 5924473 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 10001 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp3ybbsd23/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 10001 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 10001 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2391101 | 2395146 | a | 0 | + | | chr11 | 5214786 | 5223262 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp2s6_0inu/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2391101 2395146 + 1 chr11 5214786 5223262 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2391101 2395146 1 1 chr11 5214786 5223262 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3343246 | 3347896 | a | 0 | + | | chr1 | 5742372 | 5752353 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp04zehuvv/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3343246 3347896 + 1 chr1 5742372 5752353 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3343246 3347896 1 1 chr1 5742372 5752353 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 5949 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpy6qado9n/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 5949 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 5949 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 781 | a | 0 | + | | chr1 | 1 | 781 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpg9pemnwz/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 781 + 2 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 781 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3286 | a | 0 | - | | chr1 | 1 | 3286 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp2jjd6_z8/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 3286 - 2 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 3286 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4817965 | 4827078 | a | 0 | + | | chr1 | 9799349 | 9807022 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpptcbhj6u/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4817965 4827078 + 1 chr1 9799349 9807022 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 4817965 4827078 1 1 chr1 9799349 9807022 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 7991 | a | 0 | + | | chr1 | 1 | 7991 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp9gjqdp6b/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 7991 + 2 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 7991 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6500953 | 6501655 | a | 0 | - | | chr9 | 5011538 | 5012240 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp4scxut9m/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6500953 6501655 - 1 chr9 5011538 5012240 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6500953 6501655 1 1 chr9 5011538 5012240 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2709 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp95ced0z3/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2709 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2709 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7220427 | 7228768 | a | 0 | + | | chr11 | 4263109 | 4271450 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp5u0w3wzz/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7220427 7228768 + 1 chr11 4263109 4271450 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 7220427 7228768 1 1 chr11 4263109 4271450 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 6066 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpx40y4_q5/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 6066 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 6066 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6933322 | 6936826 | a | 0 | - | | chr1 | 8297664 | 8303002 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpnoeog8or/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6933322 6936826 - 1 chr1 8297664 8303002 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6933322 6936826 1 1 chr1 8297664 8303002 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7675975 | 7676050 | a | 0 | + | | chr1 | 185898 | 195519 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp0yueej46/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 185898 195519 + 1 chr1 7675975 7676050 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 185898 195519 1 1 chr1 7675975 7676050 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8116541 | 8116543 | a | 0 | + | | chr1 | 4259720 | 4260564 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpoa7v9sri/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4259720 4260564 + 1 chr1 8116541 8116543 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 4259720 4260564 1 1 chr1 8116541 8116543 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4062 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp97xv_e2z/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 4062 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 4062 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7238523 | 7240925 | a | 0 | + | | chr9 | 9559168 | 9561570 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp57983yqa/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7238523 7240925 + 1 chr9 9559168 9561570 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 7238523 7240925 1 1 chr9 9559168 9561570 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpn_b3j_8d/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9023115 | 9030532 | a | 0 | - | | chr1 | 6832569 | 6833952 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpkw706wi9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6832569 6833952 - 1 chr1 9023115 9030532 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6832569 6833952 1 1 chr1 9023115 9030532 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 526720 | 526722 | a | 0 | + | | chr1 | 8049371 | 8059168 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpj_t30xva/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 526720 526722 + 1 chr1 8049371 8059168 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 526720 526722 1 1 chr1 8049371 8059168 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8483345 | 8484716 | a | 0 | + | | chr1 | 8096962 | 8099472 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpagp4gxbl/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8096962 8099472 - 1 chr1 8483345 8484716 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 8096962 8099472 1 1 chr1 8483345 8484716 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8848316 | 8852070 | a | 0 | - | | chr4 | 1817447 | 1827146 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpuw8jr1km/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8848316 8852070 - 1 chr4 1817447 1827146 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 8848316 8852070 1 1 chr4 1817447 1827146 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6162130 | 6169401 | a | 0 | - | | chr1 | 6429498 | 6438074 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp3vaoqlw3/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6162130 6169401 - 1 chr1 6429498 6438074 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6162130 6169401 1 1 chr1 6429498 6438074 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 5085 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp10tsbvet/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 5085 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 5085 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1217840 | 1227550 | a | 0 | + | | chr1 | 1621701 | 1625403 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp_z01vfb3/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1217840 1227550 + 1 chr1 1621701 1625403 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1217840 1227550 1 1 chr1 1621701 1625403 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 648744 | 656882 | a | 0 | + | | chr1 | 2793179 | 2801108 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp4uxubc36/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 648744 656882 + 1 chr1 2793179 2801108 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 648744 656882 1 1 chr1 2793179 2801108 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 7573 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp1k_5i5gn/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 7573 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 7573 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 5199 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp497bssfd/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 5199 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 5199 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2971 | a | 0 | + | | chr1 | 1 | 2971 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpr7f5mz29/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2971 + 2 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2971 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2655895 | 2657748 | a | 0 | + | | chr1 | 4325287 | 4331525 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp_rt1jpne/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2655895 2657748 + 1 chr1 4325287 4331525 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2655895 2657748 1 1 chr1 4325287 4331525 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2756 | a | 0 | + | | chr1 | 1 | 2756 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp8u5y1gun/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2756 + 2 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2756 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5542724 | 5551193 | a | 0 | - | | chr1 | 5406153 | 5408398 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpdwwoyvjp/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5406153 5408398 - 1 chr1 5542724 5551193 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5406153 5408398 1 1 chr1 5542724 5551193 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7064933 | 7073854 | a | 0 | - | | chr4 | 9550835 | 9555097 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp7m4rl7f7/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7064933 7073854 - 1 chr4 9550835 9555097 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 7064933 7073854 1 1 chr4 9550835 9555097 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7736462 | 7740161 | a | 0 | - | | chr11 | 7611808 | 7612502 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp3neu46p9/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7736462 7740161 - 1 chr11 7611808 7612502 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 7736462 7740161 1 1 chr11 7611808 7612502 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6292634 | 6296782 | a | 0 | + | | chr7 | 896454 | 906241 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp9ylpmo_w/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 6292634 6296782 + 1 chr7 896454 906241 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 6292634 6296782 1 1 chr7 896454 906241 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8844357 | 8850255 | a | 0 | - | | chr1 | 446151 | 454070 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpwt02r8b1/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 446151 454070 - 1 chr1 8844357 8850255 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 446151 454070 1 1 chr1 8844357 8850255 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3782161 | 3786436 | a | 0 | - | | chr22 | 99722 | 102277 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpm96opggr/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 3782161 3786436 - 1 chr22 99722 102277 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 3782161 3786436 1 1 chr22 99722 102277 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 1710 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpid4ter_j/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 1710 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 1710 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2179530 | 2189023 | a | 0 | - | | chr16 | 2697812 | 2699064 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpv142asv5/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2179530 2189023 - 1 chr16 2697812 2699064 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2179530 2189023 1 1 chr16 2697812 2699064 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5970646 | 5971773 | a | 0 | + | | chr1 | 113247 | 115602 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpirai8uro/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 113247 115602 + 1 chr1 5970646 5971773 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 113247 115602 1 1 chr1 5970646 5971773 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2105927 | 2110286 | a | 0 | + | | chr1 | 8164745 | 8165905 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpniw9vvov/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 2105927 2110286 + 1 chr1 8164745 8165905 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 2105927 2110286 1 1 chr1 8164745 8165905 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 5516 | a | 0 | + | | chr1 | 1 | 5516 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp_rt64m1i/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 5516 + 2 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 5516 2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9988963 | 9989154 | a | 0 | + | | chr1 | 399168 | 402847 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp2i4ldvwf/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 399168 402847 - 1 chr1 9988963 9989154 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 399168 402847 1 1 chr1 9988963 9989154 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpf8xdlp3t/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 _________________________________ test_summary _________________________________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 @pytest.mark.bedtools > @settings( max_examples=max_examples, deadline=deadline, print_blob=True, suppress_health_check=HealthCheck.all()) tests/test_unary.py:311: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:322: in test_summary gr.summary() pyranges/pyranges.py:4475: in summary return _summary(self, to_stdout, return_df) pyranges/methods/summary.py:16: in _summary c = self.merge(strand=True) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_summary( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AAFBAQAAQQEAQQEAQQEAQQA=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr14', 'chr19'], 'Start': [3399638, 9508271, 1891784, 5803165, 9508271, 6072137, 5851558], 'End': [3407711, 9513825, 1893565, 5810170, 9518271, 6081995, 5857031], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '-', '-', '-', '-', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr14', 'chr19'], 'Start': [9508271, 3399638, 1891784, 5803165, 9508271, 6072137, 5851558], 'End': [9508272, 3399639, 1891785, 5803166, 9508272, 6072138, 5851559], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr14', 'chr19'], 'Start': [9508271, 3399638, 1891784, 5803165, 9508271, 6072137, 3399638], 'End': [9508272, 3399639, 1891785, 5803166, 9508272, 6072138, 3399639], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+', '+', '+']} {'Chromosome': ['chr5', 'chr5', 'chr5', 'chr5', 'chr14', 'chr19'], 'Start': [1, 1, 1, 1, 1, 1], 'End': [2, 2, 2, 2, 2, 2], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+', '+']} {'Chromosome': ['chr5', 'chr5', 'chr5', 'chr14', 'chr19'], 'Start': [1, 1, 1, 1, 1], 'End': [2, 2, 2, 2, 2], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+']} {'Chromosome': ['chr5', 'chr5', 'chr14', 'chr19'], 'Start': [1, 1, 1, 1], 'End': [2, 2, 2, 2], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1'], 'Start': [1, 1, 1, 1], 'End': [2, 2, 2, 2], 'Name': ['a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr11'], 'Start': [2584391, 2584391], 'End': [2592573, 2586539], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr11', 'chr11'], 'Start': [2584391, 2584391], 'End': [2586539, 2592573], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr8'], 'Start': [4277528, 1832828], 'End': [4278754, 1838659], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [175725, 2781712], 'End': [181424, 2789327], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr19'], 'Start': [10000000, 7929827], 'End': [10002601, 7932428], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr8'], 'Start': [3154188, 7886413], 'End': [3162011, 7888133], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [9273], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [1994038, 8505052], 'End': [1998650, 8507240], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr14'], 'Start': [2379384, 1055123], 'End': [2381184, 1058528], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [9909150, 4923381], 'End': [9912563, 4931542], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr3'], 'Start': [9999999, 8523474], 'End': [10008070, 8523475], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '+']} {'Chromosome': ['chr1', 'chr21'], 'Start': [353514, 7053560], 'End': [362887, 7060067], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 1], 'End': [4507, 4507], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr14'], 'Start': [1685945, 5168514], 'End': [1694825, 5177394], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [4423447, 7012205], 'End': [4429375, 7016874], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [5721], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [8758679, 8758679], 'End': [8764374, 8767773], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr21'], 'Start': [8065135, 9692108], 'End': [8075041, 9694230], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [1685912, 7694127], 'End': [1688093, 7698892], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr3'], 'Start': [7633865, 30602], 'End': [7640841, 31231], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [7915], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr10'], 'Start': [5001111, 1622880], 'End': [5010674, 1631742], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr16'], 'Start': [3904861, 6043437], 'End': [3909571, 6044427], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [4688971, 4688971], 'End': [4694227, 4693763], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr8'], 'Start': [639178, 7353857], 'End': [645544, 7363857], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [5474510, 6066272], 'End': [5481755, 6076272], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [2951378, 6164665], 'End': [2952542, 6165829], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [6514], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [4562486, 9889694], 'End': [4565561, 9897199], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr21'], 'Start': [3169033, 3318634], 'End': [3169034, 3318635], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [8720602, 3513734], 'End': [8729890, 3517159], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [9014234, 4209871], 'End': [9020184, 4216828], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr4'], 'Start': [9999999, 3787089], 'End': [10005002, 3789397], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [6180016, 213843], 'End': [6190016, 215007], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr3'], 'Start': [8012811, 8012811], 'End': [8020603, 8016874], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [2472628, 4539030], 'End': [2475567, 4542665], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 1], 'End': [690, 690], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr22'], 'Start': [2833454, 2], 'End': [2843389, 3026], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [3167924, 5007198], 'End': [3175541, 5007199], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr21'], 'Start': [558747, 8036121], 'End': [566799, 8044805], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chrM'], 'Start': [441006, 12812], 'End': [449822, 16680], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [82896, 2817206], 'End': [85941, 2822597], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 1], 'End': [8607, 8607], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr2'], 'Start': [8569080, 1723148], 'End': [8573774, 1730797], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [1126727, 246398], 'End': [1136562, 256271], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 1], 'End': [3328, 3328], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [5524039, 5915062], 'End': [5533447, 5924470], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [374], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr14'], 'Start': [3634552, 10000000], 'End': [3634818, 10002019], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 1], 'End': [9640, 9640], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr9'], 'Start': [9622104, 9622104], 'End': [9622700, 9631593], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr18'], 'Start': [4920952, 4920952], 'End': [4928692, 4928986], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr21'], 'Start': [2672566, 6096656], 'End': [2682228, 6097178], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 1], 'End': [2467, 2467], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr18'], 'Start': [1823885, 10000000], 'End': [1823924, 10000001], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [6120], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr21'], 'Start': [7829732, 3946359], 'End': [7831142, 3952112], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 1], 'End': [817, 817], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 1], 'End': [6072, 6072], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr8'], 'Start': [5975180, 10000000], 'End': [5978701, 10002704], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr15'], 'Start': [3647973, 3249619], 'End': [3652492, 3254479], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [1464305, 839635], 'End': [1468265, 847570], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [969022, 2568833], 'End': [970600, 2570411], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chrM'], 'Start': [9783134, 1092087], 'End': [9783136, 1098870], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [4911860, 8345588], 'End': [4919347, 8351536], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr15'], 'Start': [8013918, 8494653], 'End': [8014315, 8497761], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr2', 'chr8'], 'Start': [2947809, 7778830], 'End': [2955672, 7788830], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [4591319, 166225], 'End': [4591918, 175972], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [3852548, 3852548], 'End': [3861237, 3855346], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [903472, 6256624], 'End': [906470, 6265531], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr2'], 'Start': [2098788, 520915], 'End': [2107782, 530588], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [7872235, 3442056], 'End': [7877454, 3445436], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr19'], 'Start': [6912090, 5815058], 'End': [6916757, 5820873], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [4363], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [6679492, 6311846], 'End': [6681265, 6316771], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [2914620, 576898], 'End': [2920659, 581341], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [2906608, 9643431], 'End': [2908257, 9649516], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [9881], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr9'], 'Start': [7835615, 10000000], 'End': [7838544, 10005852], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 1], 'End': [755, 755], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr12'], 'Start': [6679029, 6887342], 'End': [6683767, 6887457], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [7616100, 7674952], 'End': [7622614, 7678137], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr16'], 'Start': [922797, 7237578], 'End': [932733, 7238241], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [4252761, 141119], 'End': [4257804, 144112], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr14'], 'Start': [9605133, 148352], 'End': [9609297, 150610], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [10000000, 3220838], 'End': [10002442, 3226875], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chrM'], 'Start': [1, 8622010], 'End': [1086, 8623381], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [7945], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [7187781, 7187781], 'End': [7191550, 7191550], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr12'], 'Start': [1666388, 4132912], 'End': [1676388, 4139438], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [10000000, 4865575], 'End': [10008449, 4873951], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr2', 'chr3'], 'Start': [6130847, 780220], 'End': [6135951, 782333], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [8608772, 2434850], 'End': [8615848, 2441894], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [7517], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [1995781, 2485668], 'End': [2003500, 2489451], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [9101064, 6670002], 'End': [9102845, 6675486], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr1'], 'Start': [7322793, 9878750], 'End': [7330189, 9879902], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '-']} {'Chromosome': ['chr1', 'chr3'], 'Start': [8285713, 8285713], 'End': [8291006, 8295638], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [654], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 1], 'End': [2184, 2184], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1', 'chr8'], 'Start': [7163451, 185370], 'End': [7167160, 189079], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['-', '-']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} __________ test_three_in_a_row[strandedness_chain429-method_chain429] __________ [gw6] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('subtract', 'overlap'), E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:207 E /usr/lib/python3/dist-packages/pandas/core/dtypes/missing.py:293 E (and 18 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ________________________________ test_windows2 _________________________________ [gw4] linux -- Python 3.13.2 /usr/bin/python3.13 def test_windows2(): c = """Chromosome Start End Count 0 chr1 10200 10400 7 1 chr1 10400 10600 7 2 chr1 51400 51600 1 3 chr1 51600 51800 3 4 chr1 51800 52000 3""" df = pd.read_csv(StringIO(c), sep=r"\s+", nrows=5) # df.End -= 1 gr = pr.PyRanges(df) print(gr) > result = gr.tile(200) tests/windows/test_windows.py:48: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pyranges/pyranges.py:4649: in tile df = pyrange_apply_single(_tiles, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/windows.py:40: in _tiles idxs, starts, ends = maketiles(df.index.values, df.Start.values, sorted_nearest/src/tiles.pyx:24: in sorted_nearest.src.tiles.maketiles ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'long' but got 'long long' sorted_nearest/src/tiles.pyx:48: ValueError ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+-----------+ | Chromosome | Start | End | Count | | (category) | (int32) | (int32) | (int64) | |--------------+-----------+-----------+-----------| | chr1 | 10200 | 10400 | 7 | | chr1 | 10400 | 10600 | 7 | | chr1 | 51400 | 51600 | 1 | | chr1 | 51600 | 51800 | 3 | | chr1 | 51800 | 52000 | 3 | +--------------+-----------+-----------+-----------+ Unstranded PyRanges object has 5 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome. __________ test_three_in_a_row[strandedness_chain423-method_chain423] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None), method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('intersect', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 9999999 | 10007519 | a | 0 | + | E | chr1 | 5103568 | 5106388 | a | 0 | + | E | chr1 | 8752820 | 8755640 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7289770 | 7289771 | a | 0 | - | E | chr1 | 6934257 | 6934258 | a | 0 | - | E | chr1 | 2070558 | 2070559 | a | 0 | - | E | chr1 | 10000000 | 10000001 | a | 0 | - | E | ... | ... | ... | ... | ... | ... | E | chr1 | 10000000 | 10000001 | a | 0 | - | E | chr1 | 2629074 | 2629075 | a | 0 | - | E | chr1 | 7960542 | 7960543 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 E (and 29 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RhaNjdwOjIyOgcu9GNgdGRAch0ZAIRDBDEABQC0S4MM6bVAxU6+96/AJeEKnFhaO3bAmQ4ySaAuE7cLCAzgFJMQATS7sw5V5jR2fLDPKA1s80YncWblRmdSy1sGJ21svUZnVk/6wDNfR3N6Kyk6Mzo7FWoCdTLBrEY5DZHZiCbh9GRFSLEAqEgrkQ4lR3B5HBkhLqbDeRukAedM899BGqFctmdNWQvgY1mdWFoiX0P1OJcWX4PLAJBTM7yM+SANjtX/EsBCzA451uvQvM5HsQAcgIj2HmMDAxQp0JEGQCGxj+m') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges 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('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10000824 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10002522 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10002816 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10002269 | a | 0 | ... | | chr1 | 10000000 | 10001896 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain419-method_chain419] __________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('nearest', 'join'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, # or any other generated value E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:73 E (and 27 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGBwBEIGIAOEGBhhIoxAggkuzgiGDABl+ARg') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') _____________________________ test_introns_single ______________________________ [gw9] linux -- Python 3.13.2 /usr/bin/python3.13 def test_introns_single(): "Assert that our fast method of computing introns is the same as the slow, correct one in compute_introns_single" gr = pr.data.gencode_gtf()[["gene_id", "Feature"]] exons = gr[gr.Feature == "exon"].merge(by="gene_id") exons.Feature = "exon" exons = exons.df df = pd.concat([gr[gr.Feature == "gene"].df, exons], sort=False) print(df) for gid, gdf in df.groupby("gene_id"): print("-------" * 20) print(gid) print(gdf) print("gdf", len(gdf)) expected = compute_introns_single(gdf, by="gene") print("expected", len(expected)) > actual = pr.PyRanges(gdf).features.introns().df tests/test_genomicfeatures.py:174: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pyranges/genomicfeatures.py:254: in introns result = pyrange_apply(_introns2, by_gr, exons, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/genomicfeatures.py:567: in _introns2 starts, ends, ids = find_introns(genes.Start.values, genes.End.values, _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' sorted_nearest/src/introns.pyx:12: ValueError ----------------------------- Captured stdout call ----------------------------- Chromosome gene_id Start End Strand Feature 0 chr1 ENSG00000223972.5 11868 14409 + gene 1 chr1 ENSG00000243485.5 29553 31109 + gene 2 chr1 ENSG00000284332.1 30365 30503 + gene 3 chr1 ENSG00000268020.3 52472 53312 + gene 4 chr1 ENSG00000240361.2 57597 64116 + gene .. ... ... ... ... ... ... 587 chr1 ENSG00000283040.1 876754 877234 - exon 588 chr1 ENSG00000283712.1 1312501 1312566 - exon 589 chr1 ENSG00000284372.1 1339649 1339708 - exon 590 chr1 ENSG00000284662.1 685678 686673 - exon 591 chr1 ENSG00000284733.1 450702 451697 - exon [711 rows x 6 columns] -------------------------------------------------------------------------------------------------------------------------------------------- ENSG00000078808.16 Chromosome gene_id Start End Strand Feature 101 chr1 ENSG00000078808.16 1216907 1232031 - gene 284 chr1 ENSG00000078808.16 1216907 1217804 - exon 285 chr1 ENSG00000078808.16 1218457 1221351 - exon 286 chr1 ENSG00000078808.16 1223243 1223357 - exon 287 chr1 ENSG00000078808.16 1223831 1223968 - exon 288 chr1 ENSG00000078808.16 1227271 1227319 - exon 289 chr1 ENSG00000078808.16 1228467 1228946 - exon 290 chr1 ENSG00000078808.16 1231891 1232031 - exon gdf 8 g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g Chromosome gene_id Start End Strand Feature 101 chr1 ENSG00000078808.16 1216907 1232031 - gene x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x Chromosome Start End gene_id Strand 0 chr1 1216907 1217804 ENSG00000078808.16 - 1 chr1 1218457 1221351 ENSG00000078808.16 - 2 chr1 1223243 1223357 ENSG00000078808.16 - 3 chr1 1223831 1223968 ENSG00000078808.16 - 4 chr1 1227271 1227319 ENSG00000078808.16 - 5 chr1 1228467 1228946 ENSG00000078808.16 - 6 chr1 1231891 1232031 ENSG00000078808.16 - expected 6 ______________________________ test_cluster[True] ______________________________ [gw0] linux -- Python 3.13.2 /usr/bin/python3.13 strand = True @pytest.mark.bedtools > @pytest.mark.parametrize("strand", [True, False]) tests/test_unary.py:96: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:132: in test_cluster result = gr.cluster(strand=strand) pyranges/pyranges.py:1070: in cluster df = pyrange_apply_single(_cluster, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/cluster.py:14: in _cluster ids = annotate_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_cluster( E strand=True, E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) sorted_nearest/src/annotate_clusters.pyx:15: Exception ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpxyr386hl/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3702626 | 3703255 | a | 0 | + | | chr1 | 8708162 | 8710779 | a | 0 | + | | chr1 | 6390423 | 6398744 | a | 0 | + | | chr1 | 9309718 | 9314927 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 8361064 | 8366537 | a | 0 | - | | chr12 | 9166547 | 9175201 | a | 0 | - | | chr16 | 6480668 | 6487991 | a | 0 | + | | chrY | 7760736 | 7766203 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpamstm2kl/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3702626 3703255 a 0 + 1 1 chr1 6390423 6398744 a 0 + 2 2 chr1 8708162 8710779 a 0 + 3 3 chr1 9309718 9314927 a 0 - 4 4 chr12 9166547 9175201 a 0 - 5 5 chr16 6480668 6487991 a 0 + 6 6 chr7 5162559 5164629 a 0 - 7 7 chr7 6480668 6484883 a 0 - 8 8 chr8 6688212 6693099 a 0 - 9 9 chr9 8361064 8366537 a 0 - 10 10 chrY 7760736 7766203 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3702626 | 3703255 | a | 0 | + | | chr1 | 8708162 | 8710779 | a | 0 | + | | chr1 | 6390423 | 6398744 | a | 0 | + | | chr1 | 9309718 | 9314927 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 8361064 | 8366537 | a | 0 | - | | chr12 | 9166547 | 9175201 | a | 0 | - | | chr16 | 6480668 | 6487991 | a | 0 | + | | chrY | 7760736 | 7766203 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3702626 | 3703255 | a | 0 | + | | chr1 | 8708162 | 8710779 | a | 0 | + | | chr1 | 6390423 | 6398744 | a | 0 | + | | chr1 | 9309718 | 9314927 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 8361064 | 8366537 | a | 0 | - | | chr12 | 9166547 | 9175201 | a | 0 | - | | chr16 | 6480668 | 6487991 | a | 0 | + | | chrY | 7760736 | 7766203 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpkbji3y84/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3702626 3703255 a 0 + 1 1 chr1 6390423 6398744 a 0 + 2 2 chr1 8708162 8710779 a 0 + 3 3 chr1 9309718 9314927 a 0 - 4 4 chr12 9166547 9175201 a 0 - 5 5 chr16 6480668 6487991 a 0 + 6 6 chr7 6480668 6484883 a 0 - 7 7 chr7 9166547 9168617 a 0 - 8 8 chr8 6688212 6693099 a 0 - 9 9 chr9 8361064 8366537 a 0 - 10 10 chrY 7760736 7766203 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3702626 | 3703255 | a | 0 | + | | chr1 | 8708162 | 8710779 | a | 0 | + | | chr1 | 6390423 | 6398744 | a | 0 | + | | chr1 | 9309718 | 9314927 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr9 | 8361064 | 8366537 | a | 0 | - | | chr12 | 9166547 | 9175201 | a | 0 | - | | chr16 | 6480668 | 6487991 | a | 0 | + | | chrY | 7760736 | 7766203 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3702626 | 3703255 | a | 0 | + | | chr1 | 8708162 | 8710779 | a | 0 | + | | chr1 | 6390423 | 6398744 | a | 0 | + | | chr1 | 9309718 | 9314927 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 9166547 | 9175201 | a | 0 | - | | chr16 | 6480668 | 6487991 | a | 0 | + | | chr16 | 9166547 | 9168617 | a | 0 | - | | chrY | 7760736 | 7766203 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpac7bomqq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3702626 3703255 a 0 + 1 1 chr1 6390423 6398744 a 0 + 2 2 chr1 8708162 8710779 a 0 + 3 3 chr1 9309718 9314927 a 0 - 4 4 chr12 9166547 9175201 a 0 - 5 5 chr16 6480668 6487991 a 0 + 6 6 chr16 9166547 9168617 a 0 - 7 7 chr7 6480668 6484883 a 0 - 8 8 chr8 6688212 6693099 a 0 - 9 9 chr9 8361064 8366537 a 0 - 10 10 chrY 7760736 7766203 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3702626 | 3703255 | a | 0 | + | | chr1 | 8708162 | 8710779 | a | 0 | + | | chr1 | 6390423 | 6398744 | a | 0 | + | | chr1 | 9309718 | 9314927 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 9166547 | 9175201 | a | 0 | - | | chr16 | 6480668 | 6487991 | a | 0 | + | | chr16 | 9166547 | 9168617 | a | 0 | - | | chrY | 7760736 | 7766203 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3702626 | 3703255 | a | 0 | + | | chr1 | 8708162 | 8710779 | a | 0 | + | | chr1 | 6390423 | 6398744 | a | 0 | + | | chr1 | 9309718 | 9314927 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 9166547 | 9175201 | a | 0 | - | | chr16 | 6480668 | 6487991 | a | 0 | + | | chr16 | 9166547 | 9168617 | a | 0 | - | | chrY | 7760736 | 7766203 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpdm2b6u4l/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3702626 3703255 a 0 + 1 1 chr1 6390423 6398744 a 0 + 2 2 chr1 8708162 8710779 a 0 + 3 3 chr1 9309718 9314927 a 0 - 4 4 chr12 9166547 9175201 a 0 - 5 5 chr16 6480668 6487991 a 0 + 6 6 chr16 9166547 9168617 a 0 - 7 7 chr7 6480668 6484883 a 0 - 8 8 chr8 6688212 6693099 a 0 - 9 9 chr9 8361064 8366537 a 0 - 10 10 chrY 7760736 7766203 a 0 - 11 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3702626 | 3703255 | a | 0 | + | | chr1 | 8708162 | 8710779 | a | 0 | + | | chr1 | 6390423 | 6398744 | a | 0 | + | | chr1 | 9309718 | 9314927 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr12 | 9166547 | 9175201 | a | 0 | - | | chr16 | 6480668 | 6487991 | a | 0 | + | | chr16 | 9166547 | 9168617 | a | 0 | - | | chrY | 7760736 | 7766203 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr7 | 1 | 2 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr12 | 1 | 2 | a | 0 | + | | chr16 | 1 | 2 | a | 0 | + | | chr16 | 1 | 2 | a | 0 | + | | chrY | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpotxwypjc/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 1 chr1 1 2 a 0 + 1 2 chr1 1 2 a 0 + 1 3 chr12 1 2 a 0 + 2 4 chr16 1 2 a 0 + 3 5 chr16 1 2 a 0 + 3 6 chr7 1 2 a 0 + 4 7 chr8 1 2 a 0 + 5 8 chr9 1 2 a 0 + 6 9 chrY 1 2 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr7 | 1 | 2 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr12 | 1 | 2 | a | 0 | + | | chr16 | 1 | 2 | a | 0 | + | | chr16 | 1 | 2 | a | 0 | + | | chrY | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr7 | 1 | 2 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr12 | 1 | 2 | a | 0 | + | | chr16 | 1 | 2 | a | 0 | + | | chr16 | 1 | 2 | a | 0 | + | | chrY | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpqrgd3eqq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 1 chr1 1 2 a 0 + 1 2 chr1 1 2 a 0 + 1 3 chr12 1 2 a 0 + 2 4 chr16 1 2 a 0 + 3 5 chr16 1 2 a 0 + 3 6 chr7 1 2 a 0 + 4 7 chr8 1 2 a 0 + 5 8 chr9 1 2 a 0 + 6 9 chrY 1 2 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr7 | 1 | 2 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr12 | 1 | 2 | a | 0 | + | | chr16 | 1 | 2 | a | 0 | + | | chr16 | 1 | 2 | a | 0 | + | | chrY | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr7 | 1 | 2 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr12 | 1 | 2 | a | 0 | + | | chr16 | 1 | 2 | a | 0 | + | | chr16 | 1 | 2 | a | 0 | + | | chrY | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpj3fusyc8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 1 chr1 1 2 a 0 + 1 2 chr1 1 2 a 0 + 1 3 chr12 1 2 a 0 + 2 4 chr16 1 2 a 0 + 3 5 chr16 1 2 a 0 + 3 6 chr7 1 2 a 0 + 4 7 chr8 1 2 a 0 + 5 8 chr9 1 2 a 0 + 6 9 chrY 1 2 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | | chr7 | 1 | 2 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr12 | 1 | 2 | a | 0 | + | | chr16 | 1 | 2 | a | 0 | + | | chr16 | 1 | 2 | a | 0 | + | | chrY | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6094868 | 6099220 | a | 0 | + | | chr7 | 3141282 | 3146693 | a | 0 | + | | chr7 | 5406203 | 5407416 | a | 0 | + | | chr7 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpx6diaz27/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6094868 6099220 a 0 + 1 1 chr7 3141282 3146693 a 0 + 2 2 chr7 5406203 5407416 a 0 + 3 3 chr7 1 2 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6094868 | 6099220 | a | 0 | + | | chr7 | 3141282 | 3146693 | a | 0 | + | | chr7 | 5406203 | 5407416 | a | 0 | + | | chr7 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6094868 | 6099220 | a | 0 | + | | chr7 | 3141282 | 3146693 | a | 0 | + | | chr7 | 1 | 2 | a | 0 | + | | chr7 | 5406203 | 5407416 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmplptiq0yc/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6094868 6099220 a 0 + 1 1 chr7 1 2 a 0 + 2 2 chr7 3141282 3146693 a 0 + 3 3 chr7 5406203 5407416 a 0 + 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6094868 | 6099220 | a | 0 | + | | chr7 | 3141282 | 3146693 | a | 0 | + | | chr7 | 1 | 2 | a | 0 | + | | chr7 | 5406203 | 5407416 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpucozzux_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpt7hjm8c6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpsgotaw77/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5035601 | 5042118 | a | 0 | - | | chr4 | 4472620 | 4474341 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp5zdt74ax/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5035601 5042118 a 0 - 1 1 chr4 4472620 4474341 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5035601 | 5042118 | a | 0 | - | | chr4 | 4472620 | 4474341 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3651190 | 3656750 | a | 0 | - | | chr6 | 8554108 | 8556668 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp556ns85w/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3651190 3656750 a 0 - 1 1 chr6 8554108 8556668 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3651190 | 3656750 | a | 0 | - | | chr6 | 8554108 | 8556668 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4556189 | 4563035 | a | 0 | + | | chr18 | 1972591 | 1974577 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmptfj6eya0/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4556189 4563035 a 0 + 1 1 chr18 1972591 1974577 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4556189 | 4563035 | a | 0 | + | | chr18 | 1972591 | 1974577 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 5512 | a | 0 | - | | chr1 | 1 | 5512 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpx5muvzpk/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 5512 a 0 - 1 1 chr1 1 5512 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 5512 | a | 0 | - | | chr1 | 1 | 5512 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 794 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp9p74ytf3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 794 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 794 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 356734 | 359198 | a | 0 | + | | chr1 | 9926800 | 9932201 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp65eerfnd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 356734 359198 a 0 + 1 1 chr1 9926800 9932201 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 356734 | 359198 | a | 0 | + | | chr1 | 9926800 | 9932201 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 951004 | 953039 | a | 0 | + | | chr1 | 540557 | 542592 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmphq5l37r5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 540557 542592 a 0 + 1 1 chr1 951004 953039 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 951004 | 953039 | a | 0 | + | | chr1 | 540557 | 542592 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4733409 | 4742637 | a | 0 | - | | chr11 | 6980822 | 6990050 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmputf86gpi/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4733409 4742637 a 0 - 1 1 chr11 6980822 6990050 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4733409 | 4742637 | a | 0 | - | | chr11 | 6980822 | 6990050 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4997 | a | 0 | + | | chr1 | 1 | 4997 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpqsntt0dx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 4997 a 0 + 1 1 chr1 1 4997 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4997 | a | 0 | + | | chr1 | 1 | 4997 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 798668 | 805025 | a | 0 | + | | chr1 | 3767447 | 3769782 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpprgupfjg/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 798668 805025 a 0 + 1 1 chr1 3767447 3769782 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 798668 | 805025 | a | 0 | + | | chr1 | 3767447 | 3769782 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8985348 | 8988204 | a | 0 | - | | chr20 | 7932013 | 7936517 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpgqhfjgnq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8985348 8988204 a 0 - 1 1 chr20 7932013 7936517 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8985348 | 8988204 | a | 0 | - | | chr20 | 7932013 | 7936517 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 486505 | 495750 | a | 0 | - | | chr11 | 486505 | 488162 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp9untthj4/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 486505 495750 a 0 - 1 1 chr11 486505 488162 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 486505 | 495750 | a | 0 | - | | chr11 | 486505 | 488162 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9576838 | 9580547 | a | 0 | + | | chr13 | 3588682 | 3596394 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpj5pkuu4o/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9576838 9580547 a 0 + 1 1 chr13 3588682 3596394 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9576838 | 9580547 | a | 0 | + | | chr13 | 3588682 | 3596394 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7986582 | 7987609 | a | 0 | + | | chr22 | 9102000 | 9108162 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp90rt2lqh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7986582 7987609 a 0 + 1 1 chr22 9102000 9108162 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7986582 | 7987609 | a | 0 | + | | chr22 | 9102000 | 9108162 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1289896 | 1295671 | a | 0 | + | | chr20 | 1289896 | 1293855 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpuib1ytw3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1289896 1295671 a 0 + 1 1 chr20 1289896 1293855 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1289896 | 1295671 | a | 0 | + | | chr20 | 1289896 | 1293855 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10004868 | a | 0 | + | | chr13 | 3785040 | 3790811 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpo2t6rx40/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 10000000 10004868 a 0 + 1 1 chr13 3785040 3790811 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10004868 | a | 0 | + | | chr13 | 3785040 | 3790811 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1555920 | 1557017 | a | 0 | - | | chr1 | 1 | 9278 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmppcgu118l/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 9278 a 0 - 1 1 chr1 1555920 1557017 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1555920 | 1557017 | a | 0 | - | | chr1 | 1 | 9278 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5869150 | 5873658 | a | 0 | - | | chr1 | 2797788 | 2807387 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp9y9yrsii/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2797788 2807387 a 0 - 1 1 chr1 5869150 5873658 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5869150 | 5873658 | a | 0 | - | | chr1 | 2797788 | 2807387 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2092951 | 2101246 | a | 0 | - | | chr1 | 8430141 | 8430142 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp945z6h5m/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2092951 2101246 a 0 - 1 1 chr1 8430141 8430142 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2092951 | 2101246 | a | 0 | - | | chr1 | 8430141 | 8430142 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 367522 | 372401 | a | 0 | + | | chr10 | 9535998 | 9539821 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpnevp52c1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 367522 372401 a 0 + 1 1 chr10 9535998 9539821 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 367522 | 372401 | a | 0 | + | | chr10 | 9535998 | 9539821 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9005868 | 9013623 | a | 0 | + | | chr11 | 4320012 | 4324517 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmplcyg1z02/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9005868 9013623 a 0 + 1 1 chr11 4320012 4324517 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9005868 | 9013623 | a | 0 | + | | chr11 | 4320012 | 4324517 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6350144 | 6359062 | a | 0 | + | | chr1 | 10000000 | 10008918 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp2n4u62xs/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6350144 6359062 a 0 + 1 1 chr1 10000000 10008918 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6350144 | 6359062 | a | 0 | + | | chr1 | 10000000 | 10008918 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp79tw2pvk/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4395 | a | 0 | + | | chr22 | 7384598 | 7388491 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp4p3p1val/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 4395 a 0 + 1 1 chr22 7384598 7388491 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4395 | a | 0 | + | | chr22 | 7384598 | 7388491 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 9087 | a | 0 | + | | chr1 | 1 | 9087 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp1qdhdi6o/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 9087 a 0 + 1 1 chr1 1 9087 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 9087 | a | 0 | + | | chr1 | 1 | 9087 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 471 | a | 0 | + | | chr1 | 1 | 471 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp3zfflnkg/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 471 a 0 + 1 1 chr1 1 471 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 471 | a | 0 | + | | chr1 | 1 | 471 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6292485 | 6301194 | a | 0 | - | | chr1 | 9326842 | 9335603 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpyucznsfd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6292485 6301194 a 0 - 1 1 chr1 9326842 9335603 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6292485 | 6301194 | a | 0 | - | | chr1 | 9326842 | 9335603 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4442403 | 4449178 | a | 0 | + | | chr2 | 5187717 | 5194221 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp6irs6knh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4442403 4449178 a 0 + 1 1 chr2 5187717 5194221 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4442403 | 4449178 | a | 0 | + | | chr2 | 5187717 | 5194221 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5240652 | 5247715 | a | 0 | - | | chr15 | 5240652 | 5242568 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpwcenc9rt/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5240652 5247715 a 0 - 1 1 chr15 5240652 5242568 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5240652 | 5247715 | a | 0 | - | | chr15 | 5240652 | 5242568 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9720616 | 9724924 | a | 0 | - | | chr1 | 3345448 | 3352180 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp7ludt9t4/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3345448 3352180 a 0 - 1 1 chr1 9720616 9724924 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9720616 | 9724924 | a | 0 | - | | chr1 | 3345448 | 3352180 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7103413 | 7112566 | a | 0 | - | | chr8 | 9373061 | 9379115 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpiipl6jzx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7103413 7112566 a 0 - 1 1 chr8 9373061 9379115 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7103413 | 7112566 | a | 0 | - | | chr8 | 9373061 | 9379115 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5005452 | 5005716 | a | 0 | + | | chr19 | 1261640 | 1270867 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp8sp2ucrq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5005452 5005716 a 0 + 1 1 chr19 1261640 1270867 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5005452 | 5005716 | a | 0 | + | | chr19 | 1261640 | 1270867 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3401 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpqcct9rtu/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 3401 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 3401 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpf4waurdd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4033 | a | 0 | - | | chr1 | 1 | 4033 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpozx4dr7w/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 4033 a 0 - 1 1 chr1 1 4033 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 4033 | a | 0 | - | | chr1 | 1 | 4033 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10007485 | a | 0 | + | | chr1 | 5351452 | 5357304 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp77tdtkbg/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 10000000 10007485 a 0 + 1 1 chr1 5351452 5357304 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10007485 | a | 0 | + | | chr1 | 5351452 | 5357304 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6277596 | 6278556 | a | 0 | + | | chr1 | 9422701 | 9427571 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp9d0tspor/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6277596 6278556 a 0 + 1 1 chr1 9422701 9427571 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6277596 | 6278556 | a | 0 | + | | chr1 | 9422701 | 9427571 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1951757 | 1952245 | a | 0 | - | | chr17 | 6741331 | 6748843 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp39d4iaeh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1951757 1952245 a 0 - 1 1 chr17 6741331 6748843 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1951757 | 1952245 | a | 0 | - | | chr17 | 6741331 | 6748843 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5034832 | 5037242 | a | 0 | - | | chr19 | 7573135 | 7573481 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpuzk4r_pj/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5034832 5037242 a 0 - 1 1 chr19 7573135 7573481 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5034832 | 5037242 | a | 0 | - | | chr19 | 7573135 | 7573481 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 9723 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp_a_z6ma_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 9723 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 9723 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1449914 | 1456674 | a | 0 | + | | chr12 | 4664014 | 4671710 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpq5uy3e7e/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1449914 1456674 a 0 + 1 1 chr12 4664014 4671710 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1449914 | 1456674 | a | 0 | + | | chr12 | 4664014 | 4671710 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6816879 | 6820974 | a | 0 | + | | chr1 | 1196400 | 1199022 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmppr_pprjo/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1196400 1199022 a 0 + 1 1 chr1 6816879 6820974 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6816879 | 6820974 | a | 0 | + | | chr1 | 1196400 | 1199022 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2569756 | 2577590 | a | 0 | + | | chr1 | 8042834 | 8049680 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpjn8x66wf/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2569756 2577590 a 0 + 1 1 chr1 8042834 8049680 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2569756 | 2577590 | a | 0 | + | | chr1 | 8042834 | 8049680 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3081827 | 3086722 | a | 0 | - | | chr1 | 7118385 | 7126394 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp7_br8xiq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3081827 3086722 a 0 - 1 1 chr1 7118385 7126394 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3081827 | 3086722 | a | 0 | - | | chr1 | 7118385 | 7126394 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1292112 | 1294736 | a | 0 | + | | chr8 | 8412279 | 8415488 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpvt13p38u/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1292112 1294736 a 0 + 1 1 chr8 8412279 8415488 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1292112 | 1294736 | a | 0 | + | | chr8 | 8412279 | 8415488 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 520848 | 529696 | a | 0 | - | | chr2 | 3099561 | 3102536 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp6nobz8ug/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 520848 529696 a 0 - 1 1 chr2 3099561 3102536 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 520848 | 529696 | a | 0 | - | | chr2 | 3099561 | 3102536 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4273476 | 4280764 | a | 0 | + | | chr5 | 7244883 | 7252171 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpm19gtgcq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4273476 4280764 a 0 + 1 1 chr5 7244883 7252171 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4273476 | 4280764 | a | 0 | + | | chr5 | 7244883 | 7252171 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7670996 | 7677443 | a | 0 | + | | chr1 | 9310384 | 9311411 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpzrgzadd_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7670996 7677443 a 0 + 1 1 chr1 9310384 9311411 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7670996 | 7677443 | a | 0 | + | | chr1 | 9310384 | 9311411 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1786988 | 1793066 | a | 0 | + | | chr3 | 8418197 | 8426857 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpnj8q82a7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1786988 1793066 a 0 + 1 1 chr3 8418197 8426857 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1786988 | 1793066 | a | 0 | + | | chr3 | 8418197 | 8426857 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 6085 | a | 0 | - | | chr1 | 1 | 6085 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpq6ignmob/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 6085 a 0 - 1 1 chr1 1 6085 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 6085 | a | 0 | - | | chr1 | 1 | 6085 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6579516 | 6580405 | a | 0 | - | | chr17 | 8978135 | 8978579 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp227j5nam/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6579516 6580405 a 0 - 1 1 chr17 8978135 8978579 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6579516 | 6580405 | a | 0 | - | | chr17 | 8978135 | 8978579 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4911265 | 4913023 | a | 0 | + | | chr1 | 8977428 | 8983073 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpm1cz69yp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4911265 4913023 a 0 + 1 1 chr1 8977428 8983073 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4911265 | 4913023 | a | 0 | + | | chr1 | 8977428 | 8983073 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6278509 | 6283958 | a | 0 | + | | chr1 | 5474468 | 5482298 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp41l9fjg1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6278509 6283958 a 0 + 1 1 chr1 5474468 5482298 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6278509 | 6283958 | a | 0 | + | | chr1 | 5474468 | 5482298 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9566075 | 9571493 | a | 0 | - | | chr13 | 6941244 | 6950843 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpmwlxdj2b/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9566075 9571493 a 0 - 1 1 chr13 6941244 6950843 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9566075 | 9571493 | a | 0 | - | | chr13 | 6941244 | 6950843 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8039752 | 8047607 | a | 0 | - | | chr1 | 2277079 | 2277427 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpkvf3g987/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2277079 2277427 a 0 - 1 1 chr1 8039752 8047607 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8039752 | 8047607 | a | 0 | - | | chr1 | 2277079 | 2277427 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2935 | a | 0 | + | | chr1 | 5428048 | 5433140 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpzs10x7g3/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2935 a 0 + 1 1 chr1 5428048 5433140 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2935 | a | 0 | + | | chr1 | 5428048 | 5433140 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8518084 | 8518593 | a | 0 | + | | chr1 | 7021756 | 7026831 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmplmdnqgh_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8518084 8518593 a 0 + 1 1 chr1 7021756 7026831 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8518084 | 8518593 | a | 0 | + | | chr1 | 7021756 | 7026831 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 758 | a | 0 | + | | chrX | 9789656 | 9799656 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpu838qwjo/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 758 a 0 + 1 1 chrX 9789656 9799656 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 758 | a | 0 | + | | chrX | 9789656 | 9799656 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 8820 | a | 0 | + | | chr1 | 1 | 8820 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp40ts7_2d/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 8820 a 0 + 1 1 chr1 1 8820 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 8820 | a | 0 | + | | chr1 | 1 | 8820 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2025457 | 2034535 | a | 0 | + | | chr2 | 867178 | 875887 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpk1j1uvye/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2025457 2034535 a 0 + 1 1 chr2 867178 875887 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2025457 | 2034535 | a | 0 | + | | chr2 | 867178 | 875887 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5474058 | 5478733 | a | 0 | + | | chr17 | 3896713 | 3905842 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpfk5aidwx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5474058 5478733 a 0 + 1 1 chr17 3896713 3905842 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5474058 | 5478733 | a | 0 | + | | chr17 | 3896713 | 3905842 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3258235 | 3263591 | a | 0 | + | | chr9 | 7424890 | 7431658 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp9yywk8i7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3258235 3263591 a 0 + 1 1 chr9 7424890 7431658 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3258235 | 3263591 | a | 0 | + | | chr9 | 7424890 | 7431658 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 741 | a | 0 | + | | chr1 | 1 | 741 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp4nbt1a0f/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 741 a 0 + 1 1 chr1 1 741 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 741 | a | 0 | + | | chr1 | 1 | 741 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3453683 | 3457354 | a | 0 | - | | chr1 | 1091126 | 1098513 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpw_7d55ap/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1091126 1098513 a 0 - 1 1 chr1 3453683 3457354 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3453683 | 3457354 | a | 0 | - | | chr1 | 1091126 | 1098513 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 546720 | 548470 | a | 0 | + | | chr21 | 7902522 | 7905017 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpk851qyh1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 546720 548470 a 0 + 1 1 chr21 7902522 7905017 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 546720 | 548470 | a | 0 | + | | chr21 | 7902522 | 7905017 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4233412 | 4242284 | a | 0 | + | | chr13 | 7426005 | 7432339 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp97q4eroj/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4233412 4242284 a 0 + 1 1 chr13 7426005 7432339 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4233412 | 4242284 | a | 0 | + | | chr13 | 7426005 | 7432339 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8163052 | 8168291 | a | 0 | + | | chr1 | 1467742 | 1475042 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp6ep7rpfu/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8163052 8168291 a 0 + 1 1 chr1 1467742 1475042 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8163052 | 8168291 | a | 0 | + | | chr1 | 1467742 | 1475042 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8021187 | 8023891 | a | 0 | + | | chr21 | 1250302 | 1254735 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpk96k_dh_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8021187 8023891 a 0 + 1 1 chr21 1250302 1254735 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8021187 | 8023891 | a | 0 | + | | chr21 | 1250302 | 1254735 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8522938 | 8531898 | a | 0 | + | | chr1 | 7721609 | 7730569 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpf_p_0b7t/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8522938 8531898 a 0 + 1 1 chr1 7721609 7730569 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8522938 | 8531898 | a | 0 | + | | chr1 | 7721609 | 7730569 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 457675 | 464379 | a | 0 | + | | chr1 | 1971321 | 1971986 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmplweguidd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 457675 464379 a 0 + 1 1 chr1 1971321 1971986 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 457675 | 464379 | a | 0 | + | | chr1 | 1971321 | 1971986 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9198898 | 9198901 | a | 0 | + | | chr18 | 9002698 | 9006169 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpdctw5f4m/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9198898 9198901 a 0 + 1 1 chr18 9002698 9006169 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9198898 | 9198901 | a | 0 | + | | chr18 | 9002698 | 9006169 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2279091 | 2280871 | a | 0 | + | | chr5 | 2723363 | 2725143 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpmjot4ts1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2279091 2280871 a 0 + 1 1 chr5 2723363 2725143 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2279091 | 2280871 | a | 0 | + | | chr5 | 2723363 | 2725143 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9905005 | 9912103 | a | 0 | + | | chr1 | 10000000 | 10002259 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpd7tusvz5/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9905005 9912103 a 0 + 1 1 chr1 10000000 10002259 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9905005 | 9912103 | a | 0 | + | | chr1 | 10000000 | 10002259 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 9869 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpx05k_o4y/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 9869 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 9869 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 519526 | 520807 | a | 0 | + | | chr1 | 8619712 | 8622573 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmptfzl3lm4/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 519526 520807 a 0 + 1 1 chr1 8619712 8622573 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 519526 | 520807 | a | 0 | + | | chr1 | 8619712 | 8622573 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7771850 | 7774553 | a | 0 | - | | chr1 | 7771850 | 7778331 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpaipqfqrh/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7771850 7774553 a 0 - 1 1 chr1 7771850 7778331 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7771850 | 7774553 | a | 0 | - | | chr1 | 7771850 | 7778331 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 726315 | 729047 | a | 0 | + | | chr1 | 7256626 | 7266205 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp227gj1f7/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 726315 729047 a 0 + 1 1 chr1 7256626 7266205 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 726315 | 729047 | a | 0 | + | | chr1 | 7256626 | 7266205 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9398401 | 9402747 | a | 0 | + | | chr5 | 3103066 | 3111437 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpqeuojprt/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 9398401 9402747 a 0 + 1 1 chr5 3103066 3111437 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9398401 | 9402747 | a | 0 | + | | chr5 | 3103066 | 3111437 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10009557 | a | 0 | - | | chr9 | 2812968 | 2822525 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpu9d6urg8/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 10000000 10009557 a 0 - 1 1 chr9 2812968 2822525 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 10000000 | 10009557 | a | 0 | - | | chr9 | 2812968 | 2822525 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 7908 | a | 0 | - | | chr1 | 1 | 7908 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpqrqoqd2l/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 7908 a 0 - 1 1 chr1 1 7908 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 7908 | a | 0 | - | | chr1 | 1 | 7908 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8217244 | 8221838 | a | 0 | - | | chr22 | 385467 | 392541 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpgd5xc8ss/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8217244 8221838 a 0 - 1 1 chr22 385467 392541 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8217244 | 8221838 | a | 0 | - | | chr22 | 385467 | 392541 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4009133 | 4018283 | a | 0 | - | | chr1 | 2337166 | 2345541 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpuf2j5xae/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2337166 2345541 a 0 - 1 1 chr1 4009133 4018283 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4009133 | 4018283 | a | 0 | - | | chr1 | 2337166 | 2345541 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2890273 | 2894240 | a | 0 | + | | chr1 | 5304734 | 5309114 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpe4jchprd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2890273 2894240 a 0 + 1 1 chr1 5304734 5309114 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2890273 | 2894240 | a | 0 | + | | chr1 | 5304734 | 5309114 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3913056 | 3915818 | a | 0 | - | | chr12 | 9239551 | 9246717 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpr4o9228i/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3913056 3915818 a 0 - 1 1 chr12 9239551 9246717 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3913056 | 3915818 | a | 0 | - | | chr12 | 9239551 | 9246717 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1975086 | 1976868 | a | 0 | - | | chr5 | 4616495 | 4619137 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpm8nmg0ur/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1975086 1976868 a 0 - 1 1 chr5 4616495 4619137 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1975086 | 1976868 | a | 0 | - | | chr5 | 4616495 | 4619137 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4655135 | 4655174 | a | 0 | - | | chr19 | 9889399 | 9891818 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmphfsp5bxq/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4655135 4655174 a 0 - 1 1 chr19 9889399 9891818 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4655135 | 4655174 | a | 0 | - | | chr19 | 9889399 | 9891818 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8261128 | 8265514 | a | 0 | + | | chr1 | 7074192 | 7075624 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp0ovlazxp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8261128 8265514 a 0 + 1 1 chr1 7074192 7075624 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8261128 | 8265514 | a | 0 | + | | chr1 | 7074192 | 7075624 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8339077 | 8347771 | a | 0 | + | | chr1 | 7658454 | 7663511 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp8u6hsq1n/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 7658454 7663511 a 0 + 1 1 chr1 8339077 8347771 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8339077 | 8347771 | a | 0 | + | | chr1 | 7658454 | 7663511 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5299848 | 5304556 | a | 0 | - | | chr1 | 3340789 | 3341644 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpljtmgfv9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3340789 3341644 a 0 - 1 1 chr1 5299848 5304556 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5299848 | 5304556 | a | 0 | - | | chr1 | 3340789 | 3341644 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 87 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp2g2xh0p4/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 87 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 87 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3677007 | 3686636 | a | 0 | - | | chr21 | 4824331 | 4829044 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp2ihzd4p1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3677007 3686636 a 0 - 1 1 chr21 4824331 4829044 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3677007 | 3686636 | a | 0 | - | | chr21 | 4824331 | 4829044 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3156004 | 3156005 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpn5b_tnmr/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 1 chr1 3156004 3156005 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3156004 | 3156005 | a | 0 | + | | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2543835 | 2544501 | a | 0 | + | | chr5 | 4654205 | 4662560 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpcv35vxlt/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2543835 2544501 a 0 + 1 1 chr5 4654205 4662560 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2543835 | 2544501 | a | 0 | + | | chr5 | 4654205 | 4662560 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8177805 | 8180011 | a | 0 | + | | chr16 | 7134886 | 7138238 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpfnap_tou/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8177805 8180011 a 0 + 1 1 chr16 7134886 7138238 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8177805 | 8180011 | a | 0 | + | | chr16 | 7134886 | 7138238 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3874232 | 3884231 | a | 0 | + | | chr1 | 5021097 | 5030610 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp2usazaq9/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3874232 3884231 a 0 + 1 1 chr1 5021097 5030610 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3874232 | 3884231 | a | 0 | + | | chr1 | 5021097 | 5030610 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 333627 | 336867 | a | 0 | + | | chr1 | 8686947 | 8687874 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp_24v4u7l/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 333627 336867 a 0 + 1 1 chr1 8686947 8687874 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 333627 | 336867 | a | 0 | + | | chr1 | 8686947 | 8687874 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8442658 | 8443011 | a | 0 | - | | chr12 | 4776515 | 4776868 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp36qv86jp/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 8442658 8443011 a 0 - 1 1 chr12 4776515 4776868 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8442658 | 8443011 | a | 0 | - | | chr12 | 4776515 | 4776868 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4817441 | 4824907 | a | 0 | + | | chr21 | 4817441 | 4817497 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpzx0azd_2/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4817441 4824907 a 0 + 1 1 chr21 4817441 4817497 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4817441 | 4824907 | a | 0 | + | | chr21 | 4817441 | 4817497 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2422184 | 2422535 | a | 0 | + | | chr1 | 2518589 | 2527954 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp5ltm4m9g/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2422184 2422535 a 0 + 1 1 chr1 2518589 2527954 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2422184 | 2422535 | a | 0 | + | | chr1 | 2518589 | 2527954 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4080910 | 4086292 | a | 0 | - | | chr6 | 3856268 | 3861282 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmp6s8vwch2/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 4080910 4086292 a 0 - 1 1 chr6 3856268 3861282 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4080910 | 4086292 | a | 0 | - | | chr6 | 3856268 | 3861282 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpx5pa5c2j/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. __________ test_three_in_a_row[strandedness_chain430-method_chain430] __________ [gw10] linux -- Python 3.13.2 /usr/bin/python3.13 + Exception Group Traceback (most recent call last): | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341, in from_call | result: TResult | None = func() | ~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 242, in | lambda: runtest_hook(item=item, **kwds), when=when, reraise=reraise | ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 182, in _multicall | return outcome.get_result() | ~~~~~~~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/pluggy/_result.py", line 100, in get_result | raise exc.with_traceback(exc.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 92, in pytest_runtest_call | yield from thread_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/threadexception.py", line 68, in thread_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 95, in pytest_runtest_call | yield from unraisable_exception_runtest_hook() | File "/usr/lib/python3/dist-packages/_pytest/unraisableexception.py", line 70, in unraisable_exception_runtest_hook | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 846, in pytest_runtest_call | yield from self._runtest_for(item, "call") | File "/usr/lib/python3/dist-packages/_pytest/logging.py", line 829, in _runtest_for | yield | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/capture.py", line 898, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall | teardown.throw(outcome._exception) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/_pytest/skipping.py", line 257, in pytest_runtest_call | return (yield) | ^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 174, in pytest_runtest_call | item.runtest() | ~~~~~~~~~~~~^^ | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1627, in runtest | self.ihook.pytest_pyfunc_call(pyfuncitem=self) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513, in __call__ | return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult) | ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec | return self._inner_hookexec(hook_name, methods, kwargs, firstresult) | ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 139, in _multicall | raise exception.with_traceback(exception.__traceback__) | File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103, in _multicall | res = hook_impl.function(*args) | File "/usr/lib/python3/dist-packages/_pytest/python.py", line 159, in pytest_pyfunc_call | result = testfunction(**testargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 40, in test_three_in_a_row | @pytest.mark.parametrize("strandedness_chain,method_chain", | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1834, in wrapped_test | raise the_error_hypothesis_found | ExceptionGroup: Hypothesis found 2 distinct failures. (2 sub-exceptions) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 82, in test_three_in_a_row | gr3 = m2(gr3, strandedness=s2) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 3023, in nearest | dfs = pyrange_apply(_nearest, self, other, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 292, in pyrange_apply | result = call_f(function, nparams, df, odf, kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 22, in call_f | return f.remote(df, odf, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 121, in _nearest | previous_r_idx, previous_dist = _previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~^ | df_to_find_nearest_in.Start, ocdf.End) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py", line 74, in _previous_nonoverlapping | r_idx, dist = nearest_previous_nonoverlapping( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ | left_starts.values, right_ends.values - 1, right_ends.index.values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/sorted_nearest.pyx", line 24, in sorted_nearest.src.sorted_nearest.nearest_previous_nonoverlapping | ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('subtract', 'nearest'), | gr=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr2=Empty PyRanges, | gr3=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 2 | 3 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:53 | (and 29 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RkZGAAYigCsR35gJiBESwBFmGCSAEAVM0D6g==') as a decorator on your test case +---------------- 2 ---------------- | Traceback (most recent call last): | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py", line 77, in test_three_in_a_row | gr2 = m1(gr2, strandedness=s1) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 4384, in subtract | other_clusters = other.merge(strand=strand) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py", line 2835, in merge | df = pyrange_apply_single(_merge, self, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 347, in pyrange_apply_single | result = call_f_single(function, nparams, df, **kwargs) | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py", line 30, in call_f_single | return f.remote(df, **kwargs) | ~~~~~~~~^^^^^^^^^^^^^^ | File "/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py", line 16, in _merge | starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) | ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "sorted_nearest/src/clusters.pyx", line 16, in sorted_nearest.src.clusters.find_clusters | Exception: Starts/Ends not int64 or int32: int64 | Falsifying example: test_three_in_a_row( | strandedness_chain=('opposite', None), | method_chain=('subtract', 'nearest'), | gr=Empty PyRanges, | gr2=+--------------+-----------+-----------+------------+-----------+--------------+ | | Chromosome | Start | End | Name | Score | Strand | | | (category) | (int64) | (int64) | (object) | (int64) | (category) | | |--------------+-----------+-----------+------------+-----------+--------------| | | chr1 | 1 | 2 | a | 0 | + | | +--------------+-----------+-----------+------------+-----------+--------------+ | Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. | For printing, the PyRanges was sorted on Chromosome and Strand., | gr3=Empty PyRanges, # or any other generated value | ) | Explanation: | These lines were always and only run by failing examples: | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:11 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/merge.py:16 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:113 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:143 | /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/multithreaded.py:30 | (and 19 more with settings.verbosity >= verbose) | | You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGIMHAAMRQxMAAACKaAlI=') as a decorator on your test case +------------------------------------ ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') __________ test_three_in_a_row[strandedness_chain435-method_chain435] __________ [gw7] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None) method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('join', 'set_intersect'), E gr=Empty PyRanges, E gr2=Empty PyRanges, # or any other generated value E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:29 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:30 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:31 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/helpers.py:39 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/getitem.py:38 E (and 136 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3BkBEMGBiDJwADEUMQAACFQAlI=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain437-method_chain437] __________ [gw2] linux -- Python 3.13.2 /usr/bin/python3.13 strandedness_chain = ('opposite', None), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E strandedness_chain=('opposite', None), E method_chain=('join', 'nearest'), E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 4373875 | 4379984 | a | 0 | + | E | chr1 | 439979 | 443860 | a | 0 | + | E | chr1 | 8587674 | 8591555 | a | 0 | + | E | chr1 | 9066856 | 9070737 | a | 0 | + | E | ... | ... | ... | ... | ... | ... | E | chr13 | 1438405 | 1444860 | a | 0 | + | E | chr14 | 9641876 | 9645757 | a | 0 | + | E | chr18 | 4985802 | 4989297 | a | 0 | + | E | chr21 | 1037367 | 1041248 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 5 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 9468582 | 9468583 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:108 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:110 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:111 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:114 E /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/nearest.py:121 E (and 30 more with settings.verbosity >= verbose) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AXicY3RhmDGtgdFZUcSJ0ZGJ0VkuzJXR2WTJL0ZnlwmXGZ3FFtgwujD0TI4Hkm0+FozOtf9mMTA6MjoyOPIwOrI6MjI6sgDZIiABIJsdSAGlmYCUIKMjG0iIAYY4EDxmoDwvkhQDA1Sfs4/wKaA+F4ZmzllA453Ztq0GucqRwdlpbzHUFCCX2YVhsvwUZAPAiNFZ9NNRoCNcGLoiM8AiLM78V8xhVoCsdxK/C1TnJAkUZHLiXc7gxK8J9g2jIyfU4WDXgbwDchSjs9ReRkZnpXW2jM6qIdmMzqEZLxhBBiEQxO1A0yEIRdCFYULVMrA4AwCXSDxr') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges 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'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3882 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | | chr1 | 1 | 3882 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _________________________________ test_windows _________________________________ [gw5] linux -- Python 3.13.2 /usr/bin/python3.13 def test_windows(): f1 = pr.data.f1() print(f1) > result = f1.tile(2) tests/windows/test_windows.py:25: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pyranges/pyranges.py:4649: in tile df = pyrange_apply_single(_tiles, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/windows.py:40: in _tiles idxs, starts, ends = maketiles(df.index.values, df.Start.values, sorted_nearest/src/tiles.pyx:24: in sorted_nearest.src.tiles.maketiles ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'long' but got 'long long' sorted_nearest/src/tiles.pyx:48: ValueError ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3 | 6 | interval1 | 0 | + | | chr1 | 8 | 9 | interval3 | 0 | + | | chr1 | 5 | 7 | interval2 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. _________________________________ test_windows _________________________________ [gw8] linux -- Python 3.13.2 /usr/bin/python3.13 @pytest.mark.bedtools > @settings( max_examples=max_examples, print_blob=True, deadline=deadline, suppress_health_check=HealthCheck.all()) tests/test_unary.py:230: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:259: in test_windows result = gr.window(10)["Chromosome Start End".split()].unstrand() pyranges/pyranges.py:5485: in window df = pyrange_apply_single(_windows, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/windows.py:11: in _windows idxs, starts, ends = makewindows(df.index.values, df.Start.values, _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_windows( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., # or any other generated value E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.127.4', b'AAFBAQAAQQEAQQEAQQEAQQA=') as a decorator on your test case sorted_nearest/src/windows.pyx:20: Exception ----------------------------- Captured stdout call ----------------------------- bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpo8dd4klf/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp3z5svrom/f1.bed) bedtools_df Chromosome Start End 0 chr1 3732797 3732807 1 chr1 3732807 3732817 2 chr1 3732817 3732827 3 chr1 3732827 3732837 4 chr1 3732837 3732847 ... ... ... ... 4596 chrX 11650 11660 4597 chrX 11660 11670 4598 chrX 11670 11680 4599 chrX 11680 11690 4600 chrX 11690 11700 [4601 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmph7fxtxux/f1.bed) bedtools_df Chromosome Start End 0 chr1 3732797 3732807 1 chr1 3732807 3732817 2 chr1 3732817 3732827 3 chr1 3732827 3732837 4 chr1 3732837 3732847 ... ... ... ... 4596 chrX 11650 11660 4597 chrX 11660 11670 4598 chrX 11670 11680 4599 chrX 11680 11690 4600 chrX 11690 11700 [4601 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpf56yufh8/f1.bed) bedtools_df Chromosome Start End 0 chr1 3732797 3732807 1 chr1 3732807 3732817 2 chr1 3732817 3732827 3 chr1 3732827 3732837 4 chr1 3732837 3732847 ... ... ... ... 4596 chr6 2313576 2313586 4597 chr6 2313586 2313596 4598 chr6 2313596 2313606 4599 chr6 2313606 2313616 4600 chr6 2313616 2313621 [4601 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp7w6ak9in/f1.bed) bedtools_df Chromosome Start End 0 chr1 3732797 3732798 1 chr1 5003046 5003047 2 chr1 6173432 6173433 3 chr10 785887 785888 4 chr17 1754451 1754452 5 chr17 2150560 2150561 6 chr19 1 2 7 chr19 8690 8691 8 chr22 6173432 6173433 9 chr6 2312116 2312117 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp7co7zmjf/f1.bed) bedtools_df Chromosome Start End 0 chr1 3732797 3732798 1 chr1 5003046 5003047 2 chr1 6173432 6173433 3 chr10 785887 785888 4 chr17 1 2 5 chr17 1754451 1754452 6 chr19 1 2 7 chr19 8690 8691 8 chr22 6173432 6173433 9 chr6 2312116 2312117 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpsp9ko7ik/f1.bed) bedtools_df Chromosome Start End 0 chr1 3732797 3732798 1 chr1 5003046 5003047 2 chr1 6173432 6173433 3 chr10 785887 785888 4 chr17 1 2 5 chr17 1754451 1754452 6 chr19 1 2 7 chr19 8690 8691 8 chr22 6173432 6173433 9 chr6 2312116 2312117 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpvime5j3k/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 1 chr10 1 2 2 chr17 1 2 3 chr17 1 2 4 chr19 1 2 5 chr19 1 2 6 chr22 1 2 7 chr6 1 2 8 chr8 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpquj_wexy/f1.bed) bedtools_df Chromosome Start End 0 chr1 8008472 8008482 1 chr1 8008482 8008492 2 chr1 8008492 8008502 3 chr1 8008502 8008512 4 chr1 8008512 8008522 ... ... ... ... 6790 chr9 9682547 9682557 6791 chr9 9682557 9682567 6792 chr9 9682567 9682577 6793 chr9 9682577 9682587 6794 chr9 9682587 9682593 [6795 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpxgr3w0d4/f1.bed) bedtools_df Chromosome Start End 0 chr1 8008472 8008482 1 chr1 8008482 8008492 2 chr1 8008492 8008502 3 chr1 8008502 8008512 4 chr1 8008512 8008522 ... ... ... ... 6790 chr9 9682547 9682557 6791 chr9 9682557 9682567 6792 chr9 9682567 9682577 6793 chr9 9682577 9682587 6794 chr9 9682587 9682593 [6795 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpizg0uzxx/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpk2u6ptvs/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpw9ohbn5h/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmppmj2vjss/f1.bed) bedtools_df Chromosome Start End 0 chr1 1081142 1081144 1 chr1 1081142 1081152 2 chr1 1081152 1081162 3 chr1 1081162 1081172 4 chr1 1081172 1081182 .. ... ... ... 369 chr1 1084822 1084832 370 chr1 1084832 1084842 371 chr1 1084842 1084852 372 chr1 1084852 1084862 373 chr1 1084862 1084865 [374 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp4ii1o0fj/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 .. ... ... ... 118 chr1 1181 1191 119 chr1 1191 1201 120 chr1 1201 1211 121 chr1 1211 1221 122 chr1 1221 1228 [123 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpomdkl8cf/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 ... ... ... ... 1303 chr1 5105780 5105790 1304 chr1 5105790 5105800 1305 chr1 5105800 5105810 1306 chr1 5105810 5105820 1307 chr1 5105820 5105827 [1308 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp9acyd625/f1.bed) bedtools_df Chromosome Start End 0 chr1 2985905 2985915 1 chr1 2985915 2985925 2 chr1 2985925 2985935 3 chr1 2985935 2985945 4 chr1 2985945 2985955 ... ... ... ... 1560 chrY 6812724 6812734 1561 chrY 6812734 6812744 1562 chrY 6812744 6812754 1563 chrY 6812754 6812764 1564 chrY 6812764 6812769 [1565 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpqa_q752h/f1.bed) bedtools_df Chromosome Start End 0 chr1 4997464 4997474 1 chr1 4997474 4997484 2 chr1 4997484 4997494 3 chr1 4997494 4997504 4 chr1 4997504 4997514 .. ... ... ... 194 chr21 3653987 3653997 195 chr21 3653997 3654007 196 chr21 3654007 3654017 197 chr21 3654017 3654027 198 chr21 3654027 3654034 [199 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpknq3ocmu/f1.bed) bedtools_df Chromosome Start End 0 chr1 593732 593742 1 chr1 593742 593752 2 chr1 593752 593762 3 chr1 593762 593772 4 chr1 593772 593782 .. ... ... ... 871 chrM 3720540 3720550 872 chrM 3720550 3720560 873 chrM 3720560 3720570 874 chrM 3720570 3720580 875 chrM 3720580 3720585 [876 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpvayfnmg0/f1.bed) bedtools_df Chromosome Start End 0 chr1 3656479 3656489 1 chr1 3656489 3656499 2 chr1 3656499 3656509 3 chr1 3656509 3656519 4 chr1 3656519 3656529 .. ... ... ... 821 chr1 4658020 4658030 822 chr1 4658030 4658040 823 chr1 4658040 4658050 824 chr1 4658050 4658060 825 chr1 4658060 4658066 [826 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmps6eludxo/f1.bed) bedtools_df Chromosome Start End 0 chr1 8199393 8199403 1 chr1 8199403 8199413 2 chr1 8199413 8199423 3 chr1 8199423 8199433 4 chr1 8199433 8199443 ... ... ... ... 1219 chr1 9925244 9925254 1220 chr1 9925254 9925264 1221 chr1 9925264 9925274 1222 chr1 9925274 9925284 1223 chr1 9925284 9925287 [1224 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpkqb5k142/f1.bed) bedtools_df Chromosome Start End 0 chr11 2636693 2636703 1 chr11 2636703 2636713 2 chr11 2636713 2636723 3 chr11 2636723 2636733 4 chr11 2636733 2636743 .. ... ... ... 720 chr2 9964198 9964208 721 chr2 9964208 9964218 722 chr2 9964218 9964228 723 chr2 9964228 9964238 724 chr2 9964238 9964246 [725 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp1u_8e2ou/f1.bed) bedtools_df Chromosome Start End 0 chr1 9608671 9608681 1 chr1 9608681 9608691 2 chr1 9608691 9608701 3 chr1 9608701 9608711 4 chr1 9608711 9608721 ... ... ... ... 1338 chr1 9616751 9616761 1339 chr1 9616761 9616771 1340 chr1 9616771 9616781 1341 chr1 9616781 9616791 1342 chr1 9616791 9616795 [1343 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpcp6gdlqt/f1.bed) bedtools_df Chromosome Start End 0 chr1 5178405 5178415 1 chr1 5178415 5178425 2 chr1 5178425 5178435 3 chr1 5178435 5178445 4 chr1 5178445 5178455 ... ... ... ... 1580 chr7 1161180 1161190 1581 chr7 1161190 1161200 1582 chr7 1161200 1161210 1583 chr7 1161210 1161220 1584 chr7 1161220 1161223 [1585 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpoqfw3ij9/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 .. ... ... ... 668 chr1 6681 6691 669 chr1 6691 6701 670 chr1 6701 6711 671 chr1 6711 6721 672 chr1 6721 6723 [673 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpv5yymanu/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 5 chr1 51 61 6 chr1 61 71 7 chr1 71 81 8 chr1 81 91 9 chr1 91 101 10 chr1 101 111 11 chr1 111 121 12 chr1 121 131 13 chr1 131 141 14 chr1 141 151 15 chr1 151 161 16 chr1 161 171 17 chr1 171 181 18 chr1 181 191 19 chr1 191 201 20 chr1 201 211 21 chr1 211 221 22 chr1 221 231 23 chr1 231 241 24 chr1 241 251 25 chr1 251 261 26 chr1 261 271 27 chr1 271 281 28 chr1 281 291 29 chr1 291 301 30 chr1 301 311 31 chr1 311 321 32 chr1 321 331 33 chr1 331 341 34 chr1 341 351 35 chr1 351 356 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpgiae5_lk/f1.bed) bedtools_df Chromosome Start End 0 chr1 1511215 1511225 1 chr1 1511225 1511235 2 chr1 1511235 1511245 3 chr1 1511245 1511255 4 chr1 1511255 1511265 ... ... ... ... 1635 chr1 2128579 2128589 1636 chr1 2128589 2128599 1637 chr1 2128599 2128609 1638 chr1 2128609 2128619 1639 chr1 2128619 2128623 [1640 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpdfj_2xxw/f1.bed) bedtools_df Chromosome Start End 0 chr1 2543937 2543947 1 chr1 2543947 2543957 2 chr1 2543957 2543967 3 chr1 2543967 2543977 4 chr1 2543977 2543987 .. ... ... ... 556 chr22 6324271 6324281 557 chr22 6324281 6324291 558 chr22 6324291 6324301 559 chr22 6324301 6324311 560 chr22 6324311 6324315 [561 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpaqkwpm0y/f1.bed) bedtools_df Chromosome Start End 0 chr1 5653942 5653952 1 chr1 5653952 5653962 2 chr1 5653962 5653972 3 chr1 5653972 5653982 4 chr1 5653982 5653992 ... ... ... ... 1253 chr1 8985744 8985754 1254 chr1 8985754 8985764 1255 chr1 8985764 8985774 1256 chr1 8985774 8985784 1257 chr1 8985784 8985786 [1258 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpd2_20ny0/f1.bed) bedtools_df Chromosome Start End 0 chr1 4439827 4439837 1 chr1 4439837 4439847 2 chr1 4439847 4439857 3 chr1 4439857 4439867 4 chr1 4439867 4439877 .. ... ... ... 127 chr16 194957 194967 128 chr16 194967 194977 129 chr16 194977 194987 130 chr16 194987 194997 131 chr16 194997 194998 [132 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpxcgtcjxw/f1.bed) bedtools_df Chromosome Start End 0 chr11 9779469 9779479 1 chr11 9779479 9779489 2 chr11 9779489 9779499 3 chr11 9779499 9779509 4 chr11 9779509 9779519 .. ... ... ... 667 chr21 9785899 9785909 668 chr21 9785909 9785919 669 chr21 9785919 9785929 670 chr21 9785929 9785939 671 chr21 9785939 9785943 [672 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpvfu2shz4/f1.bed) bedtools_df Chromosome Start End 0 chr1 2906370 2906380 1 chr1 2906380 2906390 2 chr1 2906390 2906400 3 chr1 2906400 2906410 4 chr1 2906410 2906420 ... ... ... ... 1770 chr1 4411885 4411895 1771 chr1 4411895 4411905 1772 chr1 4411905 4411915 1773 chr1 4411915 4411925 1774 chr1 4411925 4411933 [1775 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp8pnasn9x/f1.bed) bedtools_df Chromosome Start End 0 chr1 4410503 4410513 1 chr1 4410513 4410523 2 chr1 4410523 4410533 3 chr1 4410533 4410541 4 chr1 8705708 8705718 .. ... ... ... 523 chr1 8710898 8710908 524 chr1 8710908 8710918 525 chr1 8710918 8710928 526 chr1 8710928 8710938 527 chr1 8710938 8710942 [528 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpem7g4o4z/f1.bed) bedtools_df Chromosome Start End 0 chr1 1158050 1158060 1 chr1 1158060 1158070 2 chr1 1158070 1158080 3 chr1 1158080 1158090 4 chr1 1158090 1158100 ... ... ... ... 1084 chr1 7148144 7148154 1085 chr1 7148154 7148164 1086 chr1 7148164 7148174 1087 chr1 7148174 7148184 1088 chr1 7148184 7148185 [1089 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpe42edq9x/f1.bed) bedtools_df Chromosome Start End 0 chr1 4561430 4561440 1 chr1 4561440 4561450 2 chr1 4561450 4561460 3 chr1 4561460 4561470 4 chr1 4561470 4561480 .. ... ... ... 421 chr16 674176 674186 422 chr16 674186 674196 423 chr16 674196 674206 424 chr16 674206 674216 425 chr16 674216 674217 [426 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpgu608z85/f1.bed) bedtools_df Chromosome Start End 0 chr1 4541260 4541270 1 chr1 4541270 4541280 2 chr1 4541280 4541290 3 chr1 4541290 4541300 4 chr1 4541300 4541310 ... ... ... ... 1279 chr16 3546735 3546745 1280 chr16 3546745 3546755 1281 chr16 3546755 3546765 1282 chr16 3546765 3546775 1283 chr16 3546775 3546777 [1284 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpdpn1b82i/f1.bed) bedtools_df Chromosome Start End 0 chr1 9445157 9445167 1 chr1 9445167 9445177 2 chr1 9445177 9445187 3 chr1 9445187 9445197 4 chr1 9445197 9445207 .. ... ... ... 913 chr1 9454287 9454297 914 chr1 9454297 9454307 915 chr1 9454307 9454317 916 chr1 9454317 9454321 917 chr4 2204686 2204688 [918 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpyduhr3sb/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 .. ... ... ... 606 chr1 6061 6071 607 chr1 6071 6081 608 chr1 6081 6091 609 chr1 6091 6101 610 chr1 6101 6106 [611 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpc64n809u/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 ... ... ... ... 1723 chr1 8591 8601 1724 chr1 8601 8611 1725 chr1 8611 8621 1726 chr1 8621 8631 1727 chr1 8631 8637 [1728 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmplm52a270/f1.bed) bedtools_df Chromosome Start End 0 chr1 5640729 5640739 1 chr1 5640739 5640749 2 chr1 5640749 5640759 3 chr1 5640759 5640769 4 chr1 5640769 5640779 ... ... ... ... 1144 chr1 7123579 7123589 1145 chr1 7123589 7123599 1146 chr1 7123599 7123609 1147 chr1 7123609 7123619 1148 chr1 7123619 7123628 [1149 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp7je74xob/f1.bed) bedtools_df Chromosome Start End 0 chr1 188227 188237 1 chr1 188237 188247 2 chr1 188247 188257 3 chr1 188257 188267 4 chr1 188267 188277 .. ... ... ... 891 chr4 2160144 2160154 892 chr4 2160154 2160164 893 chr4 2160164 2160174 894 chr4 2160174 2160184 895 chr4 2160184 2160193 [896 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpai9_sgm6/f1.bed) bedtools_df Chromosome Start End 0 chr1 991258 991268 1 chr1 991268 991278 2 chr1 991278 991288 3 chr1 991288 991298 4 chr1 991298 991308 ... ... ... ... 1345 chr1 1475685 1475695 1346 chr1 1475695 1475705 1347 chr1 1475705 1475715 1348 chr1 1475715 1475725 1349 chr1 1475725 1475731 [1350 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpabsxrb90/f1.bed) bedtools_df Chromosome Start End 0 chr1 3784777 3784787 1 chr1 3784787 3784797 2 chr1 3784797 3784807 3 chr1 3784807 3784817 4 chr1 3784817 3784827 ... ... ... ... 1537 chr11 4954755 4954765 1538 chr11 4954765 4954775 1539 chr11 4954775 4954785 1540 chr11 4954785 4954795 1541 chr11 4954795 4954799 [1542 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpwbk8_z_d/f1.bed) bedtools_df Chromosome Start End 0 chr1 3347077 3347087 1 chr1 3347087 3347097 2 chr1 3347097 3347107 3 chr1 3347107 3347117 4 chr1 3347117 3347127 ... ... ... ... 1126 chr1 7298904 7298914 1127 chr1 7298914 7298924 1128 chr1 7298924 7298934 1129 chr1 7298934 7298944 1130 chr1 7298944 7298951 [1131 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpn9qixl8z/f1.bed) bedtools_df Chromosome Start End 0 chr1 3085561 3085571 1 chr1 3085571 3085581 2 chr1 3085581 3085591 3 chr1 3085591 3085601 4 chr1 3085601 3085611 .. ... ... ... 558 chr1 3091141 3091151 559 chr1 3091151 3091161 560 chr1 3091161 3091171 561 chr1 3091171 3091181 562 chr1 3091181 3091188 [563 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpxddu5nt6/f1.bed) bedtools_df Chromosome Start End 0 chr1 846114 846124 1 chr1 846124 846134 2 chr1 846134 846144 3 chr1 846144 846154 4 chr1 846154 846164 5 chr1 846164 846174 6 chr1 846174 846184 7 chr1 846184 846194 8 chr1 846194 846204 9 chr1 846204 846214 10 chr1 846214 846224 11 chr1 846224 846234 12 chr1 846234 846244 13 chr1 846244 846254 14 chr1 846254 846264 15 chr1 4240314 4240324 16 chr1 4240324 4240334 17 chr1 4240334 4240344 18 chr1 4240344 4240354 19 chr1 4240354 4240364 20 chr1 4240364 4240374 21 chr1 4240374 4240384 22 chr1 4240384 4240394 23 chr1 4240394 4240404 24 chr1 4240404 4240414 25 chr1 4240414 4240424 26 chr1 4240424 4240434 27 chr1 4240434 4240444 28 chr1 4240444 4240454 29 chr1 4240454 4240464 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpehwa8p74/f1.bed) bedtools_df Chromosome Start End 0 chr1 151811 151821 1 chr1 151821 151831 2 chr1 151831 151841 3 chr1 151841 151851 4 chr1 151851 151861 .. ... ... ... 880 chr17 1824972 1824982 881 chr17 1824982 1824992 882 chr17 1824992 1825002 883 chr17 1825002 1825012 884 chr17 1825012 1825017 [885 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmptwhmuv1f/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 .. ... ... ... 713 chr1 3541 3551 714 chr1 3551 3561 715 chr1 3561 3571 716 chr1 3571 3581 717 chr1 3581 3584 [718 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp7uv9yjkp/f1.bed) bedtools_df Chromosome Start End 0 chr1 7929682 7929692 1 chr1 7929692 7929702 2 chr1 7929702 7929712 3 chr1 7929712 7929722 4 chr1 7929722 7929732 .. ... ... ... 363 chr4 5217819 5217829 364 chr4 5217829 5217839 365 chr4 5217839 5217849 366 chr4 5217849 5217859 367 chr4 5217859 5217867 [368 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmptljsbk8o/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 .. ... ... ... 125 chr1 1251 1261 126 chr1 1261 1271 127 chr1 1271 1281 128 chr1 1281 1291 129 chr1 1291 1295 [130 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpg9iihmk6/f1.bed) bedtools_df Chromosome Start End 0 chr1 1063735 1063745 1 chr1 1063745 1063755 2 chr1 1063755 1063765 3 chr1 1063765 1063775 4 chr1 1063775 1063785 ... ... ... ... 1685 chr1 6551970 6551980 1686 chr1 6551980 6551990 1687 chr1 6551990 6552000 1688 chr1 6552000 6552010 1689 chr1 6552010 6552013 [1690 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpgw_k11sb/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 .. ... ... ... 295 chr1 2951 2961 296 chr1 2961 2971 297 chr1 2971 2981 298 chr1 2981 2991 299 chr1 2991 3001 [300 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpjopfo4s3/f1.bed) bedtools_df Chromosome Start End 0 chr1 2319267 2319277 1 chr1 2319277 2319287 2 chr1 2319287 2319297 3 chr1 2319297 2319307 4 chr1 2319307 2319317 .. ... ... ... 96 chr1 9025817 9025827 97 chr1 9025827 9025837 98 chr1 9025837 9025847 99 chr1 9025847 9025857 100 chr1 9025857 9025867 [101 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmphu5pq1s4/f1.bed) bedtools_df Chromosome Start End 0 chr1 5443177 5443187 1 chr1 5443187 5443197 2 chr1 5443197 5443207 3 chr1 5443207 5443217 4 chr1 5443217 5443227 ... ... ... ... 1855 chr21 2579620 2579630 1856 chr21 2579630 2579640 1857 chr21 2579640 2579650 1858 chr21 2579650 2579660 1859 chr21 2579660 2579666 [1860 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp7atfm8mm/f1.bed) bedtools_df Chromosome Start End 0 chr1 884314 884324 1 chr1 884324 884334 2 chr1 884334 884344 3 chr1 884344 884354 4 chr1 884354 884364 .. ... ... ... 972 chr1 9629693 9629703 973 chr1 9629703 9629713 974 chr1 9629713 9629723 975 chr1 9629723 9629733 976 chr1 9629733 9629737 [977 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp2bj6t3xu/f1.bed) bedtools_df Chromosome Start End 0 chr1 527115 527125 1 chr1 527125 527135 2 chr1 527135 527145 3 chr1 527145 527155 4 chr1 527155 527165 ... ... ... ... 1005 chr1 2417253 2417263 1006 chr1 2417263 2417273 1007 chr1 2417273 2417283 1008 chr1 2417283 2417293 1009 chr1 2417293 2417301 [1010 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp97dom1el/f1.bed) bedtools_df Chromosome Start End 0 chr1 434061 434071 1 chr1 434071 434081 2 chr1 434081 434091 3 chr1 434091 434101 4 chr1 434101 434111 ... ... ... ... 1436 chr1 9401164 9401174 1437 chr1 9401174 9401184 1438 chr1 9401184 9401194 1439 chr1 9401194 9401204 1440 chr1 9401204 9401208 [1441 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp8oc40vtg/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 .. ... ... ... 462 chr1 6877278 6877288 463 chr1 6877288 6877298 464 chr1 6877298 6877308 465 chr1 6877308 6877318 466 chr1 6877318 6877327 [467 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpsqi8logl/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 .. ... ... ... 189 chr1 1891 1901 190 chr1 1901 1911 191 chr1 1911 1921 192 chr1 1921 1931 193 chr1 1931 1938 [194 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpoxh0yu90/f1.bed) bedtools_df Chromosome Start End 0 chr1 2583581 2583591 1 chr1 2583591 2583601 2 chr1 2583601 2583611 3 chr1 2583611 2583621 4 chr1 2583621 2583631 ... ... ... ... 1516 chr7 5161 5171 1517 chr7 5171 5181 1518 chr7 5181 5191 1519 chr7 5191 5201 1520 chr7 5201 5207 [1521 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpb50_w13n/f1.bed) bedtools_df Chromosome Start End 0 chr1 2612550 2612560 1 chr1 2612560 2612570 2 chr1 2612570 2612580 3 chr1 2612580 2612590 4 chr1 2612590 2612600 .. ... ... ... 409 chr1 2616640 2616650 410 chr1 2616650 2616660 411 chr1 2616660 2616670 412 chr1 2616670 2616680 413 chr1 2616680 2616686 [414 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpovt4s2aj/f1.bed) bedtools_df Chromosome Start End 0 chr1 4289059 4289069 1 chr1 4289069 4289079 2 chr1 4289079 4289089 3 chr1 4289089 4289099 4 chr1 4289099 4289109 .. ... ... ... 223 chr1 5336924 5336934 224 chr1 5336934 5336944 225 chr1 5336944 5336954 226 chr1 5336954 5336964 227 chr1 5336964 5336972 [228 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpp9vr2211/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpdoihzktg/f1.bed) bedtools_df Chromosome Start End 0 chr1 3902655 3902656 1 chr1 7433160 7433170 2 chr1 7433170 7433180 3 chr1 7433180 7433190 4 chr1 7433190 7433200 .. ... ... ... 535 chr1 7438500 7438510 536 chr1 7438510 7438520 537 chr1 7438520 7438530 538 chr1 7438530 7438540 539 chr1 7438540 7438549 [540 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpqt15ajd0/f1.bed) bedtools_df Chromosome Start End 0 chr1 5196078 5196088 1 chr1 5196088 5196098 2 chr1 5196098 5196108 3 chr1 5196108 5196118 4 chr1 5196118 5196128 .. ... ... ... 983 chr1 5205908 5205918 984 chr1 5205918 5205928 985 chr1 5205928 5205938 986 chr1 5205938 5205948 987 chr1 9852446 9852447 [988 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpp2_td7gg/f1.bed) bedtools_df Chromosome Start End 0 chr1 2330252 2330262 1 chr1 2330262 2330272 2 chr1 2330272 2330282 3 chr1 2330282 2330292 4 chr1 2330292 2330302 ... ... ... ... 1083 chr1 3563062 3563072 1084 chr1 3563072 3563082 1085 chr1 3563082 3563092 1086 chr1 3563092 3563102 1087 chr1 3563102 3563105 [1088 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpo28g15es/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 ... ... ... ... 1347 chr1 6711 6721 1348 chr1 6721 6731 1349 chr1 6731 6741 1350 chr1 6741 6751 1351 chr1 6751 6752 [1352 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp6_4ynsg3/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 .. ... ... ... 749 chr1 7491 7501 750 chr1 7501 7511 751 chr1 7511 7521 752 chr1 7521 7531 753 chr1 7531 7538 [754 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp7s81mxwx/f1.bed) bedtools_df Chromosome Start End 0 chr1 2 12 1 chr1 12 22 2 chr1 22 32 3 chr1 32 42 4 chr1 42 52 ... ... ... ... 1930 chr1 900222 900232 1931 chr1 900232 900242 1932 chr1 900242 900252 1933 chr1 900252 900262 1934 chr1 900262 900265 [1935 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpvw_c18y_/f1.bed) bedtools_df Chromosome Start End 0 chr1 2408700 2408710 1 chr1 2408710 2408720 2 chr1 2408720 2408730 3 chr1 2408730 2408740 4 chr1 2408740 2408750 ... ... ... ... 1790 chr1 8827343 8827353 1791 chr1 8827353 8827363 1792 chr1 8827363 8827373 1793 chr1 8827373 8827383 1794 chr1 8827383 8827392 [1795 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpwwgxvb7b/f1.bed) bedtools_df Chromosome Start End 0 chr1 8479594 8479604 1 chr1 8479604 8479614 2 chr1 8479614 8479624 3 chr1 8479624 8479634 4 chr1 8479634 8479644 ... ... ... ... 1602 chr1 9068990 9069000 1603 chr1 9069000 9069010 1604 chr1 9069010 9069020 1605 chr1 9069020 9069030 1606 chr1 9069030 9069038 [1607 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpxy18xfpy/f1.bed) bedtools_df Chromosome Start End 0 chr1 900823 900833 1 chr1 900833 900843 2 chr1 900843 900853 3 chr1 900853 900863 4 chr1 900863 900873 ... ... ... ... 1196 chr10 6473358 6473368 1197 chr10 6473368 6473378 1198 chr10 6473378 6473388 1199 chr10 6473388 6473398 1200 chr10 6473398 6473407 [1201 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp3e4_w00_/f1.bed) bedtools_df Chromosome Start End 0 chr1 4000560 4000570 1 chr1 4000570 4000580 2 chr1 4000580 4000590 3 chr1 4000590 4000600 4 chr1 4000600 4000610 ... ... ... ... 1271 chr1 8594883 8594893 1272 chr1 8594893 8594903 1273 chr1 8594903 8594913 1274 chr1 8594913 8594923 1275 chr1 8594923 8594925 [1276 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpn6ik5r3u/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 .. ... ... ... 911 chr1 9111 9121 912 chr1 9121 9131 913 chr1 9131 9141 914 chr1 9141 9151 915 chr1 9151 9155 [916 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpo1qzhtuw/f1.bed) bedtools_df Chromosome Start End 0 chr1 800838 800848 1 chr1 800848 800858 2 chr1 800858 800868 3 chr1 800868 800878 4 chr1 800878 800888 ... ... ... ... 1013 chr1 3546154 3546164 1014 chr1 3546164 3546174 1015 chr1 3546174 3546184 1016 chr1 3546184 3546194 1017 chr1 3546194 3546202 [1018 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpgpz4t7tf/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 5 chr1 51 61 6 chr1 61 71 7 chr1 71 81 8 chr1 81 91 9 chr1 91 101 10 chr1 101 111 11 chr1 111 121 12 chr1 121 131 13 chr1 131 141 14 chr1 141 151 15 chr1 151 161 16 chr1 161 171 17 chr1 171 181 18 chr1 181 188 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp0n9ev8vt/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 .. ... ... ... 906 chr1 9061 9071 907 chr1 9071 9081 908 chr1 9081 9091 909 chr1 9091 9101 910 chr1 9101 9106 [911 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpmzdgxwgk/f1.bed) bedtools_df Chromosome Start End 0 chr1 8681566 8681576 1 chr1 8681576 8681586 2 chr1 8681586 8681596 3 chr1 8681596 8681606 4 chr1 8681606 8681616 .. ... ... ... 848 chr17 8684166 8684176 849 chr17 8684176 8684186 850 chr17 8684186 8684196 851 chr17 8684196 8684206 852 chr17 8684206 8684214 [853 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp0l1g1c11/f1.bed) bedtools_df Chromosome Start End 0 chr1 5222073 5222083 1 chr1 5222083 5222093 2 chr1 5222093 5222103 3 chr1 5222103 5222113 4 chr1 5222113 5222123 ... ... ... ... 1473 chr1 8484798 8484808 1474 chr1 8484808 8484818 1475 chr1 8484818 8484828 1476 chr1 8484828 8484838 1477 chr1 8484838 8484843 [1478 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpvuraxn4t/f1.bed) bedtools_df Chromosome Start End 0 chr1 1374676 1374686 1 chr1 1374686 1374696 2 chr1 1374696 1374706 3 chr1 1374706 1374716 4 chr1 1374716 1374726 ... ... ... ... 1537 chr1 4902458 4902468 1538 chr1 4902468 4902478 1539 chr1 4902478 4902488 1540 chr1 4902488 4902498 1541 chr1 4902498 4902507 [1542 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmphf4fzhve/f1.bed) bedtools_df Chromosome Start End 0 chr1 1072557 1072558 1 chr1 1072557 1072558 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpv3wbvgzl/f1.bed) bedtools_df Chromosome Start End 0 chr1 8869696 8869698 1 chr1 8869696 8869706 2 chr1 8869706 8869716 3 chr1 8869716 8869726 4 chr1 8869726 8869736 .. ... ... ... 366 chr1 8873346 8873356 367 chr1 8873356 8873366 368 chr1 8873366 8873376 369 chr1 8873376 8873386 370 chr1 8873386 8873390 [371 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpsit_97ro/f1.bed) bedtools_df Chromosome Start End 0 chr1 8188710 8188720 1 chr1 8188720 8188730 2 chr1 8188730 8188740 3 chr1 8188740 8188750 4 chr1 8188750 8188760 .. ... ... ... 514 chrX 2291951 2291961 515 chrX 2291961 2291971 516 chrX 2291971 2291981 517 chrX 2291981 2291991 518 chrX 2291991 2291992 [519 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmptwxm98uj/f1.bed) bedtools_df Chromosome Start End 0 chr1 3687477 3687487 1 chr1 3687487 3687497 2 chr1 3687497 3687507 3 chr1 3687507 3687517 4 chr1 3687517 3687527 ... ... ... ... 1101 chr1 6361609 6361619 1102 chr1 6361619 6361629 1103 chr1 6361629 6361639 1104 chr1 6361639 6361649 1105 chr1 6361649 6361650 [1106 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpzj1t0ude/f1.bed) bedtools_df Chromosome Start End 0 chr1 3263600 3263610 1 chr1 3263610 3263620 2 chr1 3263620 3263630 3 chr1 3263630 3263640 4 chr1 3263640 3263650 ... ... ... ... 1158 chr14 8171161 8171171 1159 chr14 8171171 8171181 1160 chr14 8171181 8171191 1161 chr14 8171191 8171201 1162 chr14 8171201 8171203 [1163 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpkq4r4ig5/f1.bed) bedtools_df Chromosome Start End 0 chr1 1514367 1514377 1 chr1 1514377 1514387 2 chr1 1514387 1514397 3 chr1 1514397 1514407 4 chr1 1514407 1514417 .. ... ... ... 897 chr12 3496849 3496859 898 chr12 3496859 3496869 899 chr12 3496869 3496879 900 chr12 3496879 3496889 901 chr12 3496889 3496890 [902 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp53l3uin0/f1.bed) bedtools_df Chromosome Start End 0 chr1 1016427 1016437 1 chr1 1016437 1016447 2 chr1 1016447 1016457 3 chr1 1016457 1016467 4 chr1 1016467 1016477 ... ... ... ... 1656 chr1 1751845 1751855 1657 chr1 1751855 1751865 1658 chr1 1751865 1751875 1659 chr1 1751875 1751885 1660 chr1 1751885 1751890 [1661 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpy10v6q4e/f1.bed) bedtools_df Chromosome Start End 0 chr1 2537240 2537250 1 chr1 2537250 2537260 2 chr1 2537260 2537270 3 chr1 2537270 2537280 4 chr1 2537280 2537290 5 chr1 2537290 2537300 6 chr1 2537300 2537310 7 chr1 2537310 2537320 8 chr1 2537320 2537330 9 chr1 2537330 2537340 10 chr1 2537340 2537350 11 chr1 2537350 2537360 12 chr1 2537360 2537370 13 chr1 2537370 2537380 14 chr1 2537380 2537390 15 chr1 2537390 2537400 16 chr1 2537400 2537402 17 chr1 3432064 3432074 18 chr1 3432074 3432084 19 chr1 3432084 3432094 20 chr1 3432094 3432104 21 chr1 3432104 3432114 22 chr1 3432114 3432124 23 chr1 3432124 3432134 24 chr1 3432134 3432144 25 chr1 3432144 3432154 26 chr1 3432154 3432164 27 chr1 3432164 3432174 28 chr1 3432174 3432184 29 chr1 3432184 3432194 30 chr1 3432194 3432204 31 chr1 3432204 3432214 32 chr1 3432214 3432224 33 chr1 3432224 3432234 34 chr1 3432234 3432244 35 chr1 3432244 3432254 36 chr1 3432254 3432264 37 chr1 3432264 3432274 38 chr1 3432274 3432284 39 chr1 3432284 3432294 40 chr1 3432294 3432304 41 chr1 3432304 3432314 42 chr1 3432314 3432324 43 chr1 3432324 3432334 44 chr1 3432334 3432344 45 chr1 3432344 3432354 46 chr1 3432354 3432364 47 chr1 3432364 3432374 48 chr1 3432374 3432384 49 chr1 3432384 3432394 50 chr1 3432394 3432404 51 chr1 3432404 3432414 52 chr1 3432414 3432424 53 chr1 3432424 3432434 54 chr1 3432434 3432444 55 chr1 3432444 3432449 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpd63x21k4/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 5 chr1 51 61 6 chr1 61 71 7 chr1 71 81 8 chr1 81 91 9 chr1 91 101 10 chr1 101 111 11 chr1 111 121 12 chr1 121 131 13 chr1 131 141 14 chr1 141 151 15 chr1 151 161 16 chr1 161 171 17 chr1 171 181 18 chr1 181 191 19 chr1 191 201 20 chr1 201 211 21 chr1 211 218 22 chr1 1 11 23 chr1 11 21 24 chr1 21 31 25 chr1 31 41 26 chr1 41 51 27 chr1 51 61 28 chr1 61 71 29 chr1 71 81 30 chr1 81 91 31 chr1 91 101 32 chr1 101 111 33 chr1 111 121 34 chr1 121 131 35 chr1 131 141 36 chr1 141 151 37 chr1 151 161 38 chr1 161 171 39 chr1 171 181 40 chr1 181 191 41 chr1 191 201 42 chr1 201 211 43 chr1 211 218 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp6im_km9u/f1.bed) bedtools_df Chromosome Start End 0 chr1 4501927 4501937 1 chr1 4501937 4501947 2 chr1 4501947 4501957 3 chr1 4501957 4501967 4 chr1 4501967 4501977 .. ... ... ... 995 chr1 9983401 9983411 996 chr1 9983411 9983421 997 chr1 9983421 9983431 998 chr1 9983431 9983441 999 chr1 9983441 9983451 [1000 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpt4ca0xsy/f1.bed) bedtools_df Chromosome Start End 0 chr1 6191939 6191949 1 chr1 6191949 6191959 2 chr1 6191959 6191969 3 chr1 6191969 6191979 4 chr1 6191979 6191989 ... ... ... ... 1368 chr1 7810849 7810859 1369 chr1 7810859 7810869 1370 chr1 7810869 7810879 1371 chr1 7810879 7810889 1372 chr1 7810889 7810892 [1373 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpuqvhfh4b/f1.bed) bedtools_df Chromosome Start End 0 chr1 422571 422581 1 chr1 422581 422591 2 chr1 422591 422601 3 chr1 422601 422611 4 chr1 422611 422621 ... ... ... ... 1003 chr1 9319556 9319566 1004 chr1 9319566 9319576 1005 chr1 9319576 9319586 1006 chr1 9319586 9319596 1007 chr1 9319596 9319598 [1008 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpul66kf20/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 .. ... ... ... 255 chr1 1251 1261 256 chr1 1261 1271 257 chr1 1271 1281 258 chr1 1281 1291 259 chr1 1291 1301 [260 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp8p7439tz/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 .. ... ... ... 59 chr1 591 601 60 chr1 601 611 61 chr1 611 621 62 chr1 621 631 63 chr1 631 640 [64 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpz3icdzey/f1.bed) bedtools_df Chromosome Start End 0 chr1 3567823 3567833 1 chr1 3567833 3567843 2 chr1 3567843 3567853 3 chr1 3567853 3567863 4 chr1 3567863 3567873 ... ... ... ... 1435 chr16 1759242 1759252 1436 chr16 1759252 1759262 1437 chr16 1759262 1759272 1438 chr16 1759272 1759282 1439 chr16 1759282 1759286 [1440 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpqkm8x0_d/f1.bed) bedtools_df Chromosome Start End 0 chr1 4209863 4209873 1 chr1 4209873 4209883 2 chr1 4209883 4209893 3 chr1 4209893 4209903 4 chr1 4209903 4209913 .. ... ... ... 532 chr11 4212063 4212073 533 chr11 4212073 4212083 534 chr11 4212083 4212093 535 chr11 4212093 4212103 536 chr11 4212103 4212112 [537 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpekpzxdzu/f1.bed) bedtools_df Chromosome Start End 0 chr1 6734240 6734250 1 chr1 6734250 6734260 2 chr1 6734260 6734270 3 chr1 6734270 6734280 4 chr1 6734280 6734290 .. ... ... ... 748 chr22 2065519 2065529 749 chr22 2065529 2065539 750 chr22 2065539 2065549 751 chr22 2065549 2065559 752 chr22 2065559 2065564 [753 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmprmaeleir/f1.bed) bedtools_df Chromosome Start End 0 chr1 5313199 5313209 1 chr1 5313209 5313219 2 chr1 5313219 5313229 3 chr1 5313229 5313239 4 chr1 5313239 5313249 ... ... ... ... 1051 chr1 6007181 6007191 1052 chr1 6007191 6007201 1053 chr1 6007201 6007211 1054 chr1 6007211 6007221 1055 chr1 6007221 6007225 [1056 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpjbwc7y7b/f1.bed) bedtools_df Chromosome Start End 0 chr1 8717562 8717572 1 chr1 8717572 8717582 2 chr1 8717582 8717592 3 chr1 8717592 8717602 4 chr1 8717602 8717612 ... ... ... ... 1028 chr1 9395117 9395127 1029 chr1 9395127 9395137 1030 chr1 9395137 9395147 1031 chr1 9395147 9395157 1032 chr1 9395157 9395164 [1033 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpzeeqpa77/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 .. ... ... ... 466 chr1 4661 4671 467 chr1 4671 4681 468 chr1 4681 4691 469 chr1 4691 4701 470 chr1 4701 4710 [471 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpr7o0t4wn/f1.bed) bedtools_df Chromosome Start End 0 chr1 1300576 1300586 1 chr1 1300586 1300596 2 chr1 1300596 1300606 3 chr1 1300606 1300616 4 chr1 1300616 1300626 ... ... ... ... 1334 chr14 31319 31329 1335 chr14 31329 31339 1336 chr14 31339 31349 1337 chr14 31349 31359 1338 chr14 31359 31364 [1339 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmplc3la4jq/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 .. ... ... ... 785 chr1 7851 7861 786 chr1 7861 7871 787 chr1 7871 7881 788 chr1 7881 7891 789 chr1 7891 7895 [790 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmptbzxk0lx/f1.bed) bedtools_df Chromosome Start End 0 chr1 6862997 6863007 1 chr1 6863007 6863017 2 chr1 6863017 6863027 3 chr1 6863027 6863037 4 chr1 6863037 6863047 ... ... ... ... 1276 chr15 6929889 6929899 1277 chr15 6929899 6929909 1278 chr15 6929909 6929919 1279 chr15 6929919 6929929 1280 chr15 6929929 6929934 [1281 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpv393k_an/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 .. ... ... ... 507 chr1 2511 2521 508 chr1 2521 2531 509 chr1 2531 2541 510 chr1 2541 2551 511 chr1 2551 2555 [512 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpwx4wzfum/f1.bed) bedtools_df Chromosome Start End 0 chr1 8556253 8556263 1 chr1 8556263 8556273 2 chr1 8556273 8556283 3 chr1 8556283 8556293 4 chr1 8556293 8556303 ... ... ... ... 1827 chr2 1954903 1954913 1828 chr2 1954913 1954923 1829 chr2 1954923 1954933 1830 chr2 1954933 1954943 1831 chr2 1954943 1954951 [1832 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpvafddr33/f1.bed) bedtools_df Chromosome Start End 0 chr1 8593901 8593911 1 chr1 8593911 8593921 2 chr1 8593921 8593931 3 chr1 8593931 8593941 4 chr1 8593941 8593951 .. ... ... ... 298 chr2 642854 642864 299 chr2 642864 642874 300 chr2 642874 642884 301 chr2 642884 642894 302 chr2 642894 642895 [303 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmperv8w95s/f1.bed) bedtools_df Chromosome Start End 0 chr1 3559061 3559071 1 chr1 3559071 3559081 2 chr1 3559081 3559091 3 chr1 3559091 3559101 4 chr1 3559101 3559111 ... ... ... ... 1269 chr17 5467279 5467289 1270 chr17 5467289 5467299 1271 chr17 5467299 5467309 1272 chr17 5467309 5467319 1273 chr17 5467319 5467320 [1274 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpf223eean/f1.bed) bedtools_df Chromosome Start End 0 chr1 5460514 5460524 1 chr1 5460524 5460534 2 chr1 5460534 5460544 3 chr1 5460544 5460554 4 chr1 5460554 5460564 .. ... ... ... 922 chrX 5466734 5466744 923 chrX 5466744 5466754 924 chrX 5466754 5466764 925 chrX 5466764 5466774 926 chrX 5466774 5466778 [927 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpiezvbtjn/f1.bed) bedtools_df Chromosome Start End 0 chr1 6806585 6806595 1 chr1 6806595 6806605 2 chr1 6806605 6806615 3 chr1 6806615 6806625 4 chr1 6806625 6806635 .. ... ... ... 991 chr16 6403511 6403521 992 chr16 6403521 6403531 993 chr16 6403531 6403541 994 chr16 6403541 6403551 995 chr16 6403551 6403554 [996 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp4stcq_3b/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 .. ... ... ... 951 chr1 9511 9521 952 chr1 9521 9531 953 chr1 9531 9541 954 chr1 9541 9551 955 chr1 9551 9553 [956 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpts6qwuic/f1.bed) bedtools_df Chromosome Start End 0 chr1 8070885 8070895 1 chr1 8070895 8070905 2 chr1 8070905 8070915 3 chr1 8070915 8070925 4 chr1 8070925 8070935 .. ... ... ... 902 chr1 8078405 8078415 903 chr1 8078415 8078425 904 chr1 8078425 8078435 905 chr1 8078435 8078445 906 chr1 8078445 8078451 [907 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpevd4pk36/f1.bed) bedtools_df Chromosome Start End 0 chr1 4546474 4546484 1 chr1 4546484 4546494 2 chr1 4546494 4546504 3 chr1 4546504 4546514 4 chr1 4546514 4546524 .. ... ... ... 671 chr22 2807897 2807907 672 chr22 2807907 2807917 673 chr22 2807917 2807927 674 chr22 2807927 2807937 675 chr22 2807937 2807944 [676 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmphi1w831h/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 11 1 chr1 11 21 2 chr1 21 31 3 chr1 31 41 4 chr1 41 51 ... ... ... ... 1795 chr1 8951 8961 1796 chr1 8961 8971 1797 chr1 8971 8981 1798 chr1 8981 8991 1799 chr1 8991 8997 [1800 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpev__l9ss/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 =============================== warnings summary =============================== tests/conftest.py:83 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/conftest.py:83: SyntaxWarning: invalid escape sequence '\s' sep="\s+", pyranges/__init__.py:18: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/__init__.py:18: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources tests/test_binary.py:118: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py:118: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:139: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py:139: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:160: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py:160: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:187: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py:187: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:212: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py:212: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:291: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py:291: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:329: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py:329: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:368: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py:368: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:392: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py:392: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:426: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py:426: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:516: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py:516: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:579: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py:579: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) pyranges/methods/init.py:60: 55 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_change_chromosome_custom.py: 2 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_concat.py: 8 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_count_overlaps.py: 1 warning .pybuild/cpython3_3.13_pyranges/build/tests/data/test_data.py: 9 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py: 55306 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py: 343525 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_getset_attr.py: 3 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_io.py: 4 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_pickle.py: 1 warning .pybuild/cpython3_3.13_pyranges/build/tests/test_stranded.py: 6 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py: 18177 warnings .pybuild/cpython3_3.13_pyranges/build/tests/windows/test_windows.py: 2 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_genomicfeatures.py: 4 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/init.py:60: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. return {k: v for k, v in df.groupby(grpby_key)} pyranges/methods/init.py:189: 44 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_change_chromosome_custom.py: 1 warning .pybuild/cpython3_3.13_pyranges/build/tests/test_concat.py: 7 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py: 4263 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py: 788 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_stranded.py: 2 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py: 4433 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/init.py:189: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. empty_removed = df.groupby("Chromosome") tests/test_do_not_error.py:46: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py:46: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:35: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py:35: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:100: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py:100: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:163: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py:163: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:205: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py:205: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:234: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py:234: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:272: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py:272: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:287: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py:287: HypothesisDeprecationWarning: The return_value health check is deprecated, because this is always an error. @settings( tests/test_unary.py:315: 11 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py:315: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) .pybuild/cpython3_3.13_pyranges/build/tests/test_concat.py::test_concat_stranded_unstranded /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:47: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['+', '+', '-', NaN, NaN] Categories (3, object): ['+', '-', '.']' has dtype incompatible with category, please explicitly cast to a compatible dtype first. v.loc[:, "Strand"] = type_v.cat.add_categories(["."]) .pybuild/cpython3_3.13_pyranges/build/tests/test_concat.py: 1 warning .pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py: 3702 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_stranded.py: 2 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_genomicfeatures.py: 1 warning .pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py: 4319 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/init.py:187: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. empty_removed = df.groupby(["Chromosome", "Strand"]) .pybuild/cpython3_3.13_pyranges/build/tests/test_concat.py::test_concat_unstranded_stranded /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/concat.py:47: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[NaN, NaN, NaN, '+', '-'] Categories (3, object): ['+', '-', '.']' has dtype incompatible with category, please explicitly cast to a compatible dtype first. v.loc[:, "Strand"] = type_v.cat.add_categories(["."]) .pybuild/cpython3_3.13_pyranges/build/tests/test_binary.py: 3494 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py: 84267 warnings .pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py: 5394 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/tostring2.py:31: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation. df = pd.concat([plus, minus]) .pybuild/cpython3_3.13_pyranges/build/tests/test_do_not_error.py: 3151 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/pyranges.py:3779: FutureWarning: The behavior of Series.replace (and DataFrame.replace) with CategoricalDtype is deprecated. In a future version, replace will only be used for cases that preserve the categories. To change the categories, use ser.cat.rename_categories instead. other.Strand = other.Strand.replace({"+": "-", "-": "+"}) .pybuild/cpython3_3.13_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1217804. 1221351. 1223357. 1223968. 1227319. 1228946. 1232031.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py: 2000 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py:178: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. for _, gdf in natsorted(df.groupby(groupby)): -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/test_binary.py::test_k_nearest[upstream-False-same-last] - Excep... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] FAILED tests/test_binary.py::test_k_nearest[upstream-False-False-last] - Exce... FAILED tests/test_binary.py::test_jaccard[same] - Exception: Starts/Ends not ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] FAILED tests/test_binary.py::test_set_intersect[False] - Exception: Starts/En... FAILED tests/test_binary.py::test_nearest[upstream-True-same] - ExceptionGrou... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] FAILED tests/test_binary.py::test_coverage[same] - Exception: Starts/Ends not... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] FAILED tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] - Ex... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] FAILED tests/test_binary.py::test_k_nearest[upstream-True-same-last] - Except... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] FAILED tests/test_binary.py::test_nearest[upstream-True-opposite] - Exception... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] FAILED tests/test_binary.py::test_set_intersect[same] - Exception: Starts/End... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] FAILED tests/test_binary.py::test_coverage[opposite] - Exception: Starts/Ends... FAILED tests/test_binary.py::test_k_nearest[upstream-True-False-last] - Excep... FAILED tests/test_binary.py::test_k_nearest[None-False-opposite-last] - Value... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] FAILED tests/test_binary.py::test_nearest[upstream-False-False] - ExceptionGr... FAILED tests/test_binary.py::test_k_nearest[None-False-same-last] - ValueErro... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] FAILED tests/test_binary.py::test_nearest[upstream-False-same] - ExceptionGro... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] FAILED tests/test_binary.py::test_k_nearest[None-False-False-last] - ValueErr... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] FAILED tests/test_binary.py::test_nearest[upstream-False-opposite] - Exceptio... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] FAILED tests/test_binary.py::test_k_nearest[None-True-opposite-last] - ValueE... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] FAILED tests/test_binary.py::test_k_nearest[None-True-same-last] - ValueError... FAILED tests/test_binary.py::test_set_union[False] - Exception: Starts/Ends n... FAILED tests/test_binary.py::test_subtraction[same] - Exception: Starts/Ends ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] FAILED tests/test_binary.py::test_k_nearest[None-True-False-last] - ValueErro... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] FAILED tests/test_binary.py::test_nearest[downstream-True-False] - ExceptionG... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] FAILED tests/test_binary.py::test_k_nearest_1_vs_nearest - ValueError: Buffer... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] FAILED tests/test_binary.py::test_set_union[same] - Exception: Starts/Ends no... FAILED tests/test_binary.py::test_subtraction[opposite] - Exception: Starts/E... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] FAILED tests/test_binary.py::test_nearest[downstream-True-same] - ExceptionGr... FAILED tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] FAILED tests/test_binary.py::test_subtraction[False] - Exception: Starts/Ends... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] FAILED tests/test_binary.py::test_k_nearest[downstream-False-same-last] - Exc... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] FAILED tests/test_binary.py::test_nearest[downstream-True-opposite] - Excepti... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] FAILED tests/test_binary.py::test_k_nearest[downstream-False-False-last] - Ex... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] FAILED tests/test_binary.py::test_nearest[None-True-False] - ExceptionGroup: ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] FAILED tests/test_binary.py::test_nearest[None-True-same] - ExceptionGroup: H... FAILED tests/test_binary.py::test_nearest[downstream-False-False] - Exception... FAILED tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] - ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] FAILED tests/test_binary.py::test_nearest[downstream-False-same] - ValueError... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] FAILED tests/test_binary.py::test_nearest[None-True-opposite] - ExceptionGrou... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] FAILED tests/test_binary.py::test_nearest[downstream-False-opposite] - Except... FAILED tests/test_binary.py::test_nearest[None-False-False] - ValueError: Buf... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] FAILED tests/test_binary.py::test_nearest[None-False-same] - ValueError: Buff... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] FAILED tests/test_binary.py::test_nearest[None-False-opposite] - ValueError: ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] FAILED tests/test_binary.py::test_k_nearest[downstream-True-same-last] - Exce... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] FAILED tests/test_binary.py::test_k_nearest[downstream-True-False-last] - Exc... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] FAILED tests/test_binary.py::test_jaccard[False] - Exception: Starts/Ends not... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] FAILED tests/test_binary.py::test_nearest[upstream-True-False] - ExceptionGro... FAILED tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] - E... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] FAILED tests/test_binary.py::test_coverage[False] - Exception: Starts/Ends no... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain331-method_chain331] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain290-method_chain290] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain348-method_chain348] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain344-method_chain344] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain336-method_chain336] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain332-method_chain332] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain343-method_chain343] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain345-method_chain345] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain330-method_chain330] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain333-method_chain333] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain357-method_chain357] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain350-method_chain350] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain334-method_chain334] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain346-method_chain346] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain351-method_chain351] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain335-method_chain335] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain360-method_chain360] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain347-method_chain347] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain372-method_chain372] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain369-method_chain369] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain364-method_chain364] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain383-method_chain383] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain381-method_chain381] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain385-method_chain385] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain362-method_chain362] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain384-method_chain384] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain382-method_chain382] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain370-method_chain370] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain376-method_chain376] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain386-method_chain386] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain374-method_chain374] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain380-method_chain380] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain395-method_chain395] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain371-method_chain371] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain399-method_chain399] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain393-method_chain393] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain403-method_chain403] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain392-method_chain392] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain390-method_chain390] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain396-method_chain396] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain404-method_chain404] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain394-method_chain394] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain407-method_chain407] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain400-method_chain400] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain406-method_chain406] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain401-method_chain401] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain402-method_chain402] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain398-method_chain398] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain432-method_chain432] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain409-method_chain409] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain417-method_chain417] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain415-method_chain415] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain427-method_chain427] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain413-method_chain413] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain414-method_chain414] FAILED tests/test_unary.py::test_merge[True] - Exception: Starts/Ends not int... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain418-method_chain418] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] FAILED tests/test_unary.py::test_cluster[False] - Exception: Starts/Ends not ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] FAILED tests/test_unary.py::test_merge[False] - Exception: Starts/Ends not in... FAILED tests/test_unary.py::test_summary - Exception: Starts/Ends not int64 o... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] FAILED tests/windows/test_windows.py::test_windows2 - ValueError: Buffer dtyp... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain423-method_chain423] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] FAILED tests/test_genomicfeatures.py::test_introns_single - ValueError: Buffe... FAILED tests/test_unary.py::test_cluster[True] - Exception: Starts/Ends not i... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain437-method_chain437] FAILED tests/windows/test_windows.py::test_windows - ValueError: Buffer dtype... FAILED tests/test_unary.py::test_windows - Exception: Starts/Ends not int64 o... ======== 406 failed, 125 passed, 533219 warnings in 6725.75s (1:52:05) ========= E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build; python3.13 -m pytest -v -n 11 dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13 make: *** [debian/rules:22: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/13493 and its subdirectories